miRNAselector: Basic Functionality Tutorial.
15 May 2020
Package
miRNAselector 0.1.0
Contents
1 Introduction
…
2 Setup script
The package miRNAselector has a lot of requirements that are nessesary to run all the experiments. The script below will allow to install most of them. It is highly recommended to install those packages using the code below.
If you are using our docker enviorment to learn this package you should not run this again. It would be a waste of time. [However, if you wish, you can play with the code in the notebook. Click here.](If you are using our enviorment to learn this package you can tweak this code in the interactive notebook. Click here.
Setup script:
readLines("setup.R") %>% paste0(collapse = "\n") %>% cat
#> tylko_cran = c("BiocManager","devtools","reticulate","remotes")
#> if (length(setdiff(tylko_cran, rownames(installed.packages()))) > 0) {
#> install.packages(setdiff(tylko_cran, rownames(installed.packages())), ask = F) }
#>
#> packages = c("remotes","devtools","rlang","ps","roxygen2", "plotly", "rJava", "mice","BiocManager", "MatchIt","curl",
#> "reticulate", "kableExtra","plyr","dplyr","edgeR","epiDisplay","rsq","MASS","Biocomb","caret","dplyr",
#> "pROC","ggplot2","DMwR", "doParallel", "Boruta", "spFSR", "varSelRF", "stringr", "psych", "C50", "randomForest", "doSNOW",
#> "foreach","data.table", "ROSE", "deepnet", "gridExtra", "stargazer","gplots","My.stepwise","snow", "sva", "Biobase",
#> "calibrate", "ggrepel", "networkD3", "VennDiagram","RSNNS", "kernlab", "car", "PairedData",
#> "profileR","classInt","kernlab","xgboost", "keras", "tidyverse", "cutpointr","tibble","tidyr",
#> "rpart", "party", "mgcv", "GDCRNATools", "rJava",
#> "imputeMissings", "visdat", "naniar", "stringr", "doSNOW", "R.utils", "TCGAbiolinks", "GDCRNATools",
#> "kableExtra", "VIM", "mice", "MatchIt", "XML", "rmarkdown", "xtable", "ComplexHeatmap","circlize",
#> "BiocStyle","magick", "BiocCheck","cluster")
#>
#> if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
#> BiocManager::install(setdiff(packages, rownames(installed.packages())), ask = F) }
#>
#> # Paczki z githuba
#> if("bounceR" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("STATWORX/bounceR") }
#> if("cutpointr" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("Thie1e/cutpointr") }
#> if("ggbiplot" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("vqv/ggbiplot") }
#>
#> tryCatch(
#> {
#> if(grepl("64", Sys.info()[["machine"]], fixed = TRUE)) {
#> # Keras
#> suppressWarnings(suppressMessages(require("keras", character.only = TRUE)))
#> #if (!is_keras_available()) { install_keras() }
#> if(!is_keras_available()) { install_keras(method = "conda") }
#> } else { message("\n\n!!!!! If you are not running 64-bit based machine you might experience problems with keras and tensorflow that are unrelated to this package. !!!!!\n\n") }
#>
#> },
#> error=function(cond) {
#> message(cond)
#> message("Unable to verify the correctness of keras installation. Please run keras::install_keras() later.")
#> # Choose a return value in case of error
#> return(NA)
#> },
#> warning=function(cond) {
#> message(cond)
#> message("Unable to verify the correctness of keras installation. Please run keras::install_keras() later.")
#> # Choose a return value in case of warning
#> return(NULL)
#> },
#> finally={
#>
#> }
#> )
#>
#> # miRNAselector
#> if("miRNAselector" %in% rownames(installed.packages()) == FALSE) { remotes::install_github("kstawiski/miRNAselector") }
#> message("OK! miRNAselector is installed correctly!")This code does not cover the installation of mxnet, which can be used for benchmarking of the selected miRNA sets. The mxnet is however built and installed in our docker enviorment.
You can run this code directly from GitHub:
library(devtools)
source_url("https://raw.githubusercontent.com/kstawiski/miRNAselector/master/vignettes/setup.R")As the miRNAselector package is installed we can load it easly.
library(miRNAselector)3 Getting the data
To present the package functionality, we will use the pan-cancer data from TCGA (https://portal.gdc.cancer.gov/repository). These two commands below will download and store all the necessary data in your working directory. Please note, that this process may take some time (depending on your network connection), but has to be performed only once.
ks.download_tissue_miRNA_data_from_TCGA()
ks.process_tissue_miRNA_TCGA(remove_miRNAs_with_null_var = T)Both of those function produce 2 files: tissue_miRNA_counts.csv and tissue_miRNA_logtpm.csv.
First of those files contains metadata and raw counts as declared in TCGA. The second is are log-transformed transcripts-per-million (TPM) counts.
Let’s load counts files and see its summary.
suppressWarnings(suppressMessages(library(data.table)))
suppressWarnings(suppressMessages(library(knitr)))
orginal_TCGA_data = fread("tissue_miRNA_counts.csv.gz")
orginal_TCGA_data[orginal_TCGA_data == ""] = NA
ks.table(table(orginal_TCGA_data$primary_site, orginal_TCGA_data$sample_type))| PrimaryTumor | SolidTissueNormal | |
|---|---|---|
| Adrenal gland | 80 | 0 |
| Bladder | 409 | 19 |
| Brain | 512 | 5 |
| Breast | 1078 | 104 |
| Bronchus and lung | 991 | 91 |
| Cervix uteri | 307 | 3 |
| Corpus uteri|Stomach|Other and unspecified parts of tongue|Meninges|Other and unspecified male genital organs|Colon|Connective, subcutaneous and other soft tissues|Bones, joints and articular cartilage of limbs|Ovary|Retroperitoneum and peritoneum|Peripheral nerves and autonomic nervous system|Uterus, NOS|Kidney | 259 | 0 |
| Corpus uteri|Uterus, NOS | 538 | 33 |
| Esophagus|Stomach | 184 | 13 |
| Eye and adnexa | 80 | 0 |
| Heart, mediastinum, and pleura|Bronchus and lung | 87 | 0 |
| Heart, mediastinum, and pleura|Other endocrine glands and related structures|Adrenal gland|Connective, subcutaneous and other soft tissues|Other and ill-defined sites|Spinal cord, cranial nerves, and other parts of central nervous system|Retroperitoneum and peritoneum | 179 | 3 |
| Heart, mediastinum, and pleura|Testis|Stomach|Lymph nodes|Bones, joints and articular cartilage of other and unspecified sites|Brain|Thyroid gland|Small intestine|Colon|Connective, subcutaneous and other soft tissues|Other and unspecified major salivary glands|Retroperitoneum and peritoneum|Hematopoietic and reticuloendothelial systems|Breast | 47 | 0 |
| Heart, mediastinum, and pleura|Thymus | 124 | 2 |
| Kidney | 873 | 130 |
| Liver and intrahepatic bile ducts | 372 | 50 |
| Other and ill-defined sites in lip, oral cavity and pharynx|Palate|Other and unspecified parts of tongue|Hypopharynx|Tonsil|Oropharynx|Larynx|Other and unspecified parts of mouth|Gum|Floor of mouth|Bones, joints and articular cartilage of other and unspecified sites|Lip|Base of tongue | 523 | 44 |
| Other and unspecified parts of biliary tract|Gallbladder|Liver and intrahepatic bile ducts | 36 | 9 |
| Ovary | 489 | 0 |
| Pancreas | 178 | 4 |
| Prostate gland | 494 | 52 |
| Rectosigmoid junction|Colon | 444 | 8 |
| Rectosigmoid junction|Unknown|Rectum|Colon|Connective, subcutaneous and other soft tissues | 161 | 3 |
| Skin | 97 | 2 |
| Stomach | 436 | 41 |
| Testis | 150 | 0 |
| Thyroid gland | 506 | 59 |
| Uterus, NOS | 57 | 0 |
Let’s consider a following exemplary problem..
We want to find the set of miRNAs the most specific to pancreatic cancer. We see that there are 178 cases of pancreatic cancer miRNA-seq results and only 4 solid tissue normal cases. However, we have multiple normal tissue miRNA-seq results from other projects that could be incorporated in the analysis. Let’s filter and label the samples of interest.
suppressWarnings(suppressMessages(library(dplyr)))
cancer_cases = filter(orginal_TCGA_data, primary_site == "Pancreas" & sample_type == "PrimaryTumor")
control_cases = filter(orginal_TCGA_data, sample_type == "SolidTissueNormal")The pipeline requires the variable Class with two levels (Cancer and Control) to be present in the dataset.
cancer_cases$Class = "Cancer"
control_cases$Class = "Control"
dataset = rbind(cancer_cases, control_cases)
ks.table(table(dataset$Class), col.names = c("Class", "Number of cases"))| Class | Number of cases |
|---|---|
| Cancer | 178 |
| Control | 675 |
boxplot(dataset$age_at_diagnosis ~ dataset$Class)
t.test(dataset$age_at_diagnosis ~ dataset$Class)
#>
#> Welch Two Sample t-test
#>
#> data: dataset$age_at_diagnosis by dataset$Class
#> t = 3.88, df = 360.55, p-value = 0.0001242
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#> 693.0905 2117.7294
#> sample estimates:
#> mean in group Cancer mean in group Control
#> 23782.23 22376.82
ks.table(table(dataset$gender.x, dataset$Class))| Cancer | Control | |
|---|---|---|
| female | 80 | 334 |
| male | 98 | 325 |
chisq.test(dataset$gender.x, dataset$Class)
#>
#> Pearson's Chi-squared test with Yates' continuity correction
#>
#> data: dataset$gender.x and dataset$Class
#> X-squared = 1.6241, df = 1, p-value = 0.2025There is a stistically significant difference in age between classess. The gender was not associated with class. In order to increase feature selection performance, we will try to balance the sets by performing propensity score matching.
old_dataset = dataset # backup
dataset = dataset[grepl("Adenocarcinomas", dataset$disease_type), ]
match_by = c("age_at_diagnosis", "gender.x")
tempdane = dplyr::select(dataset, match_by)
tempdane$Class = ifelse(dataset$Class == "Cancer", TRUE, FALSE)
suppressMessages(library(mice))
suppressMessages(library(MatchIt))
temp1 = mice(tempdane, m = 1)
#>
#> iter imp variable
#> 1 1 age_at_diagnosis
#> 2 1 age_at_diagnosis
#> 3 1 age_at_diagnosis
#> 4 1 age_at_diagnosis
#> 5 1 age_at_diagnosis
temp2 = temp1$data
temp3 = mice::complete(temp1)
temp3 = temp3[complete.cases(temp3), ]
tempform = ks.create_miRNA_formula(match_by)
mod_match <- matchit(tempform, data = temp3)
newdata = match.data(mod_match)
dataset = dataset[as.numeric(rownames(newdata)), ]Let’s check if there is any imbalance in the new, transformed dataset.
boxplot(dataset$age_at_diagnosis ~ dataset$Class)
t.test(dataset$age_at_diagnosis ~ dataset$Class)
#>
#> Welch Two Sample t-test
#>
#> data: dataset$age_at_diagnosis by dataset$Class
#> t = 0.090876, df = 351.63, p-value = 0.9276
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#> -827.5374 907.7172
#> sample estimates:
#> mean in group Cancer mean in group Control
#> 23782.23 23742.14
ks.table(table(dataset$gender.x, dataset$Class))| Cancer | Control | |
|---|---|---|
| female | 80 | 79 |
| male | 98 | 99 |
chisq.test(dataset$gender.x, dataset$Class)
#>
#> Pearson's Chi-squared test with Yates' continuity correction
#>
#> data: dataset$gender.x and dataset$Class
#> X-squared = 0, df = 1, p-value = 1
fwrite(dataset, "balanced_dataset.csv.gz")There are no significant differences in age or gender composition between classes now. We can proceed to standard filtering, log-transormation and TPM-normalization.
However, first, in order to stay consistent between different datasets, we need to standardise microRNA names.
ks.correct_miRNA_names() unify the miRNA names between different versions of miRbase.
dataset = ks.correct_miRNA_names(dataset) # Correct miRNA names based on the aliases. Useful when analyzing old datasets - to keep the results coherent with current knowledge.
danex = dplyr::select(dataset, starts_with("hsa")) # Create data.frame or matrix with miRNA counts with miRNAs in columns and cases in rows.
metadane = dplyr::select(dataset, -starts_with("hsa")) # Metadata with 'Class' variables.
ks.table(table(metadane$Class)) # Let's be sure that 'Class' variable is correct and contains only 'Cancer' and 'Control' cases.| Var1 | Freq |
|---|---|
| Cancer | 178 |
| Control | 178 |
ttpm = ks.counts_to_log10tpm(danex, metadane, ids = metadane$sample, filtr = T, filtr_minimalcounts = 100, filtr_howmany = 1/3) # We will leave only the miRNAs which apeared with at least 100 counts in 1/3 of cases.
#>
#> DGEList unfiltered object with TPM was saved as TPM_DGEList.rds.
#> DGEList filtered object with TPM was saved as TPM_DGEList_filtered.rds.
#> (After filtering) miRNAs left: 166 | filtered out: 2418.
#> Returned data are log10(TPM).You might have noticed, that we have filtered out microRNAs not having at least 100 counts in 1/3 of samples. It was done to ensure that microRNAs selected as features for classifier (possibly used in clinic) would be detectable in other, cheaper methods, such as qPCR. After filtering there are 166 miRNAs left.
In the next step we will devide the dataset into training, testing and validation datasets. We strongly belive that hold-out validation is the most redundant validation method and although miRNAselector supports cross-validation, the hold-out validation is set by default in most cases. Thus, the rest of the analysis is dependent on existance of 3 seperate datasets:
- Training dataset (
mixed_train.csv): By default 60%, used for differential expression, feature selection and model training. - Testing dataset (
mixed_test.csv): By default 20%, used for hyperparameter selection (inholdout=Tmode)and for performance assessment. - Validation dataset (
mixed_valid.csv): By default 20%, used only for performance assessment.
The best signiture (best set of miRNAs for diagnostic test) can be selected based on all 3 datasets, 2 datasets or only validation set. The process of best signiture selection will be discussed below.
The split can be prepared manually by user (the pipeline expects to find mixed_*.csv files in working directory) or in a convinient way using ks.prepare_split(). Let’s do it now.
mixed = ks.prepare_split(metadane = metadane, ttpm = ttpm, train_proc = 0.6)
#>
#> Saved 3 sets as csv in working directory. Retruned mixed dataset.Let’s see a split summary.
mixed = fread("mixed.csv")
ks.table(table(mixed$Class, mixed$mix))| test | train | valid | |
|---|---|---|---|
| Cancer | 36 | 107 | 35 |
| Control | 36 | 107 | 35 |
ks.table(cbind(mixed[1:10, c(100:105)], Class = mixed[1:10, "Class"]))| hsa-miR-30c-5p | hsa-miR-30c-2-3p | hsa-miR-30d-5p | hsa-miR-139-5p | hsa-miR-10a-5p | hsa-miR-10b-5p | Class.Class |
|---|---|---|---|---|---|---|
| 2.598949 | 1.514444 | 3.802908 | 1.555401 | 4.735516 | 4.298381 | Cancer |
| 2.391663 | 1.416540 | 3.656058 | 1.326116 | 4.615369 | 3.946954 | Cancer |
| 2.576255 | 1.566166 | 3.721311 | 1.220338 | 4.385001 | 3.998914 | Cancer |
| 2.260492 | 1.401010 | 3.539243 | 1.924365 | 3.945605 | 4.486228 | Cancer |
| 2.595315 | 1.562735 | 3.571441 | 1.721510 | 4.519249 | 4.126032 | Cancer |
| 2.632860 | 1.723000 | 3.708020 | 2.120359 | 4.875796 | 3.887056 | Cancer |
| 2.747742 | 2.016887 | 3.852090 | 1.533525 | 3.961177 | 3.642831 | Cancer |
| 3.037578 | 1.880192 | 3.960987 | 1.798007 | 4.675070 | 4.133894 | Cancer |
| 2.598933 | 1.291485 | 3.581714 | 1.413095 | 4.580566 | 3.960672 | Cancer |
| 2.829601 | 1.494520 | 3.589292 | 1.755581 | 4.687104 | 4.209582 | Cancer |
We can see that the dataset was devided in balanced way. Now we are ready to move to the analysis…
4 Basic exploratory analysis
In biomarker studies we relay on validation. We perform hold-out validation, so the signature selection has to be based on training dataset only. Including testing and validation dataset in the exploratory analysis could lead to bias (‘data leakage’). In the following section we show how to use our package to perform quick exploratory analysis of miRNA-seq data.
dane = ks.load_datamix(use_smote_not_rose = T) # load mixed_*.csv files
train = dane[[1]]
test = dane[[2]]
valid = dane[[3]]
train_smoted = dane[[4]]
trainx = dane[[5]]
trainx_smoted = dane[[6]] # get the objects from list to make the code more readable.ks_load_datamix() function loads the data created in preparation phase. It requires the output constructed by ks.prepare_split() function to be placed in working directory (‘wd’), thus files ‘mixed_train.csv’, ‘mixed_test.csv’ and ‘mixed_valid.csv’ have to exist in the directory.
If you have split the data manually, there may be some imbalance of classes in train, test or validation datasets. If so, ks.prepare_split() perform balancing using:
- ROSE (default): https://journal.r-project.org/archive/2014/RJ-2014-008/RJ-2014-008.pdf - by default we generate 10 * number of cases in orginal dataset.
- SMOTE: https://arxiv.org/abs/1106.1813 - by defult we use ‘perc.under=100’ and ‘k=10’.
At the beging of the analysis we usually perform principal component analysis (PCA) to assess for any batch effect, possible outliers and get a general understanding of miRNA profile. The package can construct 2-dimentional biplot and 3-dimentional interactive scatterplot based on the computed components.
pca = ks.PCA(trainx, train$Class)
pca
3D PCA plot may not be shown correctly in Jupyter notebook, but you can check in e.g. R Studio that it works.
pca3d = ks.PCA_3D(trainx, train$Class)
pca3dNow we can also correct the batch effect, if there is any. For example, you can use ks.combat() to do so. However, detailed demonstration is out of scope of this tutorial.
Usually, the next step in the exploratory analysis is to perform the differential expression analysis. Differential expression in our package is biomarker-discovery oriented, thus it uses t-test with the correction for multiple comparisons. The following table shows signifiantly differently expressed miRNAs after Benjamini-Hochberg correction.
de = ks.miRNA_differential_expression(trainx, train$Class)
sig_de = de %>% dplyr::filter(`p-value BH` <= 0.05) %>% dplyr::arrange(`p-value BH`) # leave only significant after Benjamini-Hochberg procedure and sort by ascending p-value
ks.table(sig_de)| miR | mean logtpm | median logtpm | SD logtpm | cancer mean | cancer median | cancer SD | control mean | control median | control SD | log10FC (subtr estim) | log10FC | log2FC | reversed_log10FC | reverse_log2FC | p-value | p-value Bonferroni | p-value Holm | -log10(p-value Bonferroni) | p-value BH |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| hsa.miR.21.5p | 5.081371 | 5.120977 | 0.5409456 | 5.473043 | 5.559281 | 0.3042087 | 4.689698 | 4.744446 | 0.4309906 | -0.7833450 | 0.7833450 | 2.6022157 | 0.7833450 | 2.6022157 | 0.0000000 | 0.0000000 | 0.0000000 | 32.2312221 | 0.0000000 |
| hsa.miR.30e.3p | 3.654915 | 3.620465 | 0.2922656 | 3.445100 | 3.469065 | 0.1835853 | 3.864731 | 3.891680 | 0.2215066 | 0.4196304 | -0.4196304 | -1.3939819 | -0.4196304 | -1.3939819 | 0.0000000 | 0.0000000 | 0.0000000 | 32.1422635 | 0.0000000 |
| hsa.miR.30a.3p | 3.861758 | 3.760500 | 0.5107622 | 3.494206 | 3.528067 | 0.2957390 | 4.229311 | 4.315264 | 0.4049904 | 0.7351047 | -0.7351047 | -2.4419651 | -0.7351047 | -2.4419651 | 0.0000000 | 0.0000000 | 0.0000000 | 31.8224321 | 0.0000000 |
| hsa.miR.30c.2.3p | 1.791478 | 1.685323 | 0.4609305 | 1.478041 | 1.473434 | 0.2548946 | 2.104915 | 2.062559 | 0.4044845 | 0.6268741 | -0.6268741 | -2.0824306 | -0.6268741 | -2.0824306 | 0.0000000 | 0.0000000 | 0.0000000 | 26.3237118 | 0.0000000 |
| hsa.miR.132.3p | 2.062941 | 2.061854 | 0.3206914 | 2.268277 | 2.222890 | 0.2453178 | 1.857606 | 1.842071 | 0.2476985 | -0.4106709 | 0.4106709 | 1.3642193 | 0.4106709 | 1.3642193 | 0.0000000 | 0.0000000 | 0.0000000 | 23.2892084 | 0.0000000 |
| hsa.miR.375.3p | 3.851381 | 4.088129 | 1.1312626 | 4.572062 | 4.593208 | 0.6167635 | 3.130699 | 3.420583 | 1.0689350 | -1.4413633 | 1.4413633 | 4.7881053 | 1.4413633 | 4.7881053 | 0.0000000 | 0.0000000 | 0.0000000 | 21.6930447 | 0.0000000 |
| hsa.miR.217.5p | 2.065790 | 1.932856 | 1.2184284 | 2.817892 | 2.596188 | 1.0079357 | 1.313689 | 1.247738 | 0.9084168 | -1.5042026 | 1.5042026 | 4.9968529 | 1.5042026 | 4.9968529 | 0.0000000 | 0.0000000 | 0.0000000 | 21.0021448 | 0.0000000 |
| hsa.miR.139.5p | 1.916157 | 1.919751 | 0.4638487 | 1.634747 | 1.558070 | 0.3573670 | 2.197567 | 2.204857 | 0.3804627 | 0.5628209 | -0.5628209 | -1.8696506 | -0.5628209 | -1.8696506 | 0.0000000 | 0.0000000 | 0.0000000 | 20.0671420 | 0.0000000 |
| hsa.miR.199a.5p | 3.034892 | 3.117770 | 0.3929526 | 3.267832 | 3.318017 | 0.2924584 | 2.801951 | 2.808411 | 0.3394148 | -0.4658802 | 0.4658802 | 1.5476204 | 0.4658802 | 1.5476204 | 0.0000000 | 0.0000000 | 0.0000000 | 18.7831163 | 0.0000000 |
| hsa.miR.338.3p | 2.743796 | 2.778247 | 0.4190933 | 2.991348 | 2.994550 | 0.3219668 | 2.496243 | 2.539407 | 0.3543332 | -0.4951049 | 0.4951049 | 1.6447027 | 0.4951049 | 1.6447027 | 0.0000000 | 0.0000000 | 0.0000000 | 18.6530266 | 0.0000000 |
| hsa.miR.199b.5p | 2.146095 | 2.358829 | 0.6145137 | 2.504540 | 2.573683 | 0.3567535 | 1.787650 | 1.799962 | 0.6100440 | -0.7168901 | 0.7168901 | 2.3814574 | 0.7168901 | 2.3814574 | 0.0000000 | 0.0000000 | 0.0000000 | 17.2507100 | 0.0000000 |
| hsa.miR.127.5p | 2.214220 | 2.327709 | 0.4803146 | 2.486170 | 2.478848 | 0.3020641 | 1.942270 | 1.939357 | 0.4722596 | -0.5438996 | 0.5438996 | 1.8067954 | 0.5438996 | 1.8067954 | 0.0000000 | 0.0000000 | 0.0000000 | 16.1634770 | 0.0000000 |
| hsa.miR.381.3p | 1.720930 | 1.791253 | 0.4579339 | 1.974984 | 1.949285 | 0.3353016 | 1.466877 | 1.476716 | 0.4226746 | -0.5081072 | 0.5081072 | 1.6878957 | 0.5081072 | 1.6878957 | 0.0000000 | 0.0000000 | 0.0000000 | 15.6751972 | 0.0000000 |
| hsa.miR.127.3p | 2.789656 | 2.829601 | 0.3874414 | 2.995898 | 3.006282 | 0.3147991 | 2.583413 | 2.568116 | 0.3415622 | -0.4124850 | 0.4124850 | 1.3702456 | 0.4124850 | 1.3702456 | 0.0000000 | 0.0000000 | 0.0000000 | 14.1819049 | 0.0000000 |
| hsa.miR.199a.3p | 3.431280 | 3.533249 | 0.3595668 | 3.620030 | 3.670480 | 0.2685999 | 3.242530 | 3.285480 | 0.3401837 | -0.3775004 | 0.3775004 | 1.2540293 | 0.3775004 | 1.2540293 | 0.0000000 | 0.0000000 | 0.0000000 | 13.5707699 | 0.0000000 |
| hsa.miR.181b.5p | 2.447025 | 2.523360 | 0.4131408 | 2.664941 | 2.705753 | 0.2848923 | 2.229109 | 2.205351 | 0.4073655 | -0.4358316 | 0.4358316 | 1.4478013 | 0.4358316 | 1.4478013 | 0.0000000 | 0.0000000 | 0.0000000 | 13.5990480 | 0.0000000 |
| hsa.miR.199b.3p | 3.430095 | 3.531945 | 0.3598114 | 3.619075 | 3.669630 | 0.2686093 | 3.241115 | 3.284615 | 0.3404382 | -0.3779599 | 0.3779599 | 1.2555557 | 0.3779599 | 1.2555557 | 0.0000000 | 0.0000000 | 0.0000000 | 13.5889555 | 0.0000000 |
| hsa.miR.194.5p | 3.119571 | 3.359054 | 0.8329947 | 3.562675 | 3.633752 | 0.4167141 | 2.676468 | 2.410622 | 0.9078933 | -0.8862067 | 0.8862067 | 2.9439150 | 0.8862067 | 2.9439150 | 0.0000000 | 0.0000000 | 0.0000000 | 13.2390851 | 0.0000000 |
| hsa.miR.134.5p | 2.366486 | 2.433393 | 0.4088244 | 2.572458 | 2.557931 | 0.2993653 | 2.160514 | 2.115254 | 0.4007277 | -0.4119434 | 0.4119434 | 1.3684465 | 0.4119434 | 1.3684465 | 0.0000000 | 0.0000000 | 0.0000000 | 12.1552043 | 0.0000000 |
| hsa.miR.30a.5p | 4.429837 | 4.356060 | 0.4519742 | 4.199892 | 4.226049 | 0.2683567 | 4.659782 | 4.685628 | 0.4813796 | 0.4598896 | -0.4598896 | -1.5277200 | -0.4598896 | -1.5277200 | 0.0000000 | 0.0000000 | 0.0000000 | 12.1052493 | 0.0000000 |
| hsa.miR.200a.5p | 2.480123 | 2.527551 | 0.5262405 | 2.744628 | 2.777438 | 0.3622178 | 2.215619 | 2.330898 | 0.5329388 | -0.5290086 | 0.5290086 | 1.7573286 | 0.5290086 | 1.7573286 | 0.0000000 | 0.0000000 | 0.0000000 | 11.9837197 | 0.0000000 |
| hsa.miR.136.5p | 1.426048 | 1.539528 | 0.5852494 | 1.722033 | 1.713813 | 0.2950712 | 1.130063 | 1.259715 | 0.6514071 | -0.5919692 | 0.5919692 | 1.9664791 | 0.5919692 | 1.9664791 | 0.0000000 | 0.0000000 | 0.0000000 | 11.6576372 | 0.0000000 |
| hsa.miR.192.5p | 3.474000 | 3.723466 | 0.8856187 | 3.920081 | 3.942126 | 0.4108526 | 3.027920 | 2.831424 | 1.0027511 | -0.8921615 | 0.8921615 | 2.9636965 | 0.8921615 | 2.9636965 | 0.0000000 | 0.0000000 | 0.0000000 | 11.4242384 | 0.0000000 |
| hsa.miR.451a | 2.540774 | 2.525599 | 0.6339915 | 2.233131 | 2.192706 | 0.4710976 | 2.848417 | 2.906464 | 0.6282318 | 0.6152860 | -0.6152860 | -2.0439357 | -0.6152860 | -2.0439357 | 0.0000000 | 0.0000000 | 0.0000000 | 11.0384525 | 0.0000000 |
| hsa.miR.200a.3p | 2.330223 | 2.419049 | 0.6863313 | 2.660594 | 2.674894 | 0.3970887 | 1.999851 | 2.171325 | 0.7539997 | -0.6607432 | 0.6607432 | 2.1949415 | 0.6607432 | 2.1949415 | 0.0000000 | 0.0000000 | 0.0000000 | 10.4637303 | 0.0000000 |
| hsa.miR.141.3p | 2.470222 | 2.587047 | 0.6758787 | 2.787653 | 2.835787 | 0.4142754 | 2.152790 | 2.366831 | 0.7368061 | -0.6348621 | 0.6348621 | 2.1089664 | 0.6348621 | 2.1089664 | 0.0000000 | 0.0000000 | 0.0000000 | 9.8966505 | 0.0000000 |
| hsa.miR.181c.3p | 1.549848 | 1.598609 | 0.3058360 | 1.691125 | 1.690791 | 0.2009568 | 1.408572 | 1.397065 | 0.3275293 | -0.2825529 | 0.2825529 | 0.9386203 | 0.2825529 | 0.9386203 | 0.0000000 | 0.0000000 | 0.0000000 | 9.5661290 | 0.0000000 |
| hsa.miR.30d.5p | 3.824938 | 3.786939 | 0.2585958 | 3.705810 | 3.708020 | 0.1763818 | 3.944065 | 3.950384 | 0.2731545 | 0.2382549 | -0.2382549 | -0.7914657 | -0.2382549 | -0.7914657 | 0.0000000 | 0.0000000 | 0.0000000 | 9.5425303 | 0.0000000 |
| hsa.miR.200b.3p | 2.716967 | 2.769036 | 0.5121158 | 2.949316 | 3.014389 | 0.3627291 | 2.484618 | 2.625241 | 0.5351976 | -0.4646977 | 0.4646977 | 1.5436922 | 0.4646977 | 1.5436922 | 0.0000000 | 0.0000000 | 0.0000000 | 9.2128238 | 0.0000000 |
| hsa.miR.708.3p | 1.553047 | 1.799718 | 0.7046857 | 1.878493 | 1.937453 | 0.3169286 | 1.227601 | 1.186108 | 0.8267867 | -0.6508920 | 0.6508920 | 2.1622164 | 0.6508920 | 2.1622164 | 0.0000000 | 0.0000000 | 0.0000000 | 9.1585590 | 0.0000000 |
| hsa.miR.210.3p | 2.239766 | 2.271507 | 0.6889295 | 2.547543 | 2.542301 | 0.5385826 | 1.931988 | 2.106523 | 0.6873228 | -0.6155552 | 0.6155552 | 2.0448301 | 0.6155552 | 2.0448301 | 0.0000000 | 0.0000000 | 0.0000000 | 8.9396288 | 0.0000000 |
| hsa.miR.486.5p | 2.102968 | 2.062283 | 0.6191482 | 1.830616 | 1.754483 | 0.4121882 | 2.375321 | 2.342782 | 0.6713086 | 0.5447046 | -0.5447046 | -1.8094696 | -0.5447046 | -1.8094696 | 0.0000000 | 0.0000000 | 0.0000000 | 8.4375052 | 0.0000000 |
| hsa.miR.29a.3p | 3.841416 | 3.818064 | 0.2415932 | 3.736185 | 3.745283 | 0.1796643 | 3.946646 | 3.954986 | 0.2503002 | 0.2104605 | -0.2104605 | -0.6991346 | -0.2104605 | -0.6991346 | 0.0000000 | 0.0000000 | 0.0000000 | 8.3240291 | 0.0000000 |
| hsa.miR.378a.3p | 2.550650 | 2.512377 | 0.3937521 | 2.378397 | 2.381114 | 0.2557418 | 2.722903 | 2.778885 | 0.4315532 | 0.3445063 | -0.3445063 | -1.1444252 | -0.3445063 | -1.1444252 | 0.0000000 | 0.0000000 | 0.0000000 | 8.2934009 | 0.0000000 |
| hsa.miR.379.5p | 2.828974 | 2.918613 | 0.4091041 | 3.006836 | 3.034753 | 0.2966347 | 2.651112 | 2.644205 | 0.4294792 | -0.3557240 | 0.3557240 | 1.1816895 | 0.3557240 | 1.1816895 | 0.0000000 | 0.0000000 | 0.0000000 | 8.2616630 | 0.0000000 |
| hsa.miR.141.5p | 2.216028 | 2.392275 | 0.6525748 | 2.500775 | 2.556782 | 0.3976527 | 1.931282 | 2.148570 | 0.7306892 | -0.5694928 | 0.5694928 | 1.8918140 | 0.5694928 | 1.8918140 | 0.0000000 | 0.0000000 | 0.0000000 | 8.1778863 | 0.0000000 |
| hsa.miR.21.3p | 2.950511 | 3.002843 | 0.4495447 | 3.143884 | 3.238660 | 0.3956108 | 2.757137 | 2.698429 | 0.4172376 | -0.3867473 | 0.3867473 | 1.2847466 | 0.3867473 | 1.2847466 | 0.0000000 | 0.0000000 | 0.0000000 | 8.1503082 | 0.0000000 |
| hsa.miR.337.3p | 1.498952 | 1.609902 | 0.4286748 | 1.685506 | 1.704399 | 0.2599192 | 1.312398 | 1.278140 | 0.4810808 | -0.3731072 | 0.3731072 | 1.2394354 | 0.3731072 | 1.2394354 | 0.0000000 | 0.0000000 | 0.0000000 | 8.1171714 | 0.0000000 |
| hsa.miR.144.5p | 1.799486 | 1.840358 | 0.7365132 | 1.481479 | 1.461856 | 0.4729441 | 2.117492 | 2.202314 | 0.8137450 | 0.6360122 | -0.6360122 | -2.1127868 | -0.6360122 | -2.1127868 | 0.0000000 | 0.0000000 | 0.0000000 | 8.0043727 | 0.0000000 |
| hsa.miR.429 | 1.847904 | 1.950131 | 0.7268633 | 2.162646 | 2.205144 | 0.3857231 | 1.533162 | 1.702486 | 0.8443154 | -0.6294838 | 0.6294838 | 2.0910999 | 0.6294838 | 2.0910999 | 0.0000000 | 0.0000000 | 0.0000000 | 7.8988604 | 0.0000000 |
| hsa.miR.335.3p | 1.773607 | 1.812886 | 0.3718545 | 1.932716 | 1.892784 | 0.2426583 | 1.614497 | 1.631930 | 0.4097115 | -0.3182195 | 0.3182195 | 1.0571023 | 0.3182195 | 1.0571023 | 0.0000000 | 0.0000000 | 0.0000000 | 7.8314098 | 0.0000000 |
| hsa.miR.126.5p | 2.232491 | 2.222927 | 0.4152358 | 2.056938 | 2.063790 | 0.2104761 | 2.408045 | 2.529680 | 0.4898455 | 0.3511067 | -0.3511067 | -1.1663511 | -0.3511067 | -1.1663511 | 0.0000000 | 0.0000000 | 0.0000000 | 7.3936205 | 0.0000000 |
| hsa.miR.30c.5p | 2.808698 | 2.749100 | 0.3490929 | 2.661967 | 2.661797 | 0.1963921 | 2.955429 | 2.915562 | 0.4035411 | 0.2934616 | -0.2934616 | -0.9748585 | -0.2934616 | -0.9748585 | 0.0000000 | 0.0000000 | 0.0000000 | 7.3565035 | 0.0000000 |
| hsa.miR.181a.3p | 2.106380 | 2.174268 | 0.3784895 | 2.261578 | 2.305816 | 0.2347854 | 1.951183 | 2.028792 | 0.4290792 | -0.3103947 | 0.3103947 | 1.0311087 | 0.3103947 | 1.0311087 | 0.0000000 | 0.0000001 | 0.0000001 | 6.9641475 | 0.0000000 |
| hsa.let.7c.5p | 3.419322 | 3.422382 | 0.3296842 | 3.287237 | 3.332260 | 0.2860501 | 3.551407 | 3.535984 | 0.3183740 | 0.2641699 | -0.2641699 | -0.8775535 | -0.2641699 | -0.8775535 | 0.0000000 | 0.0000002 | 0.0000001 | 6.7432319 | 0.0000000 |
| hsa.miR.181a.5p | 3.155295 | 3.246986 | 0.4050583 | 3.316282 | 3.343112 | 0.2324404 | 2.994307 | 2.991241 | 0.4725895 | -0.3219750 | 0.3219750 | 1.0695778 | 0.3219750 | 1.0695778 | 0.0000000 | 0.0000004 | 0.0000003 | 6.3623836 | 0.0000000 |
| hsa.miR.221.3p | 2.290528 | 2.336670 | 0.3527519 | 2.427381 | 2.408816 | 0.2861108 | 2.153674 | 2.182603 | 0.3610694 | -0.2737072 | 0.2737072 | 0.9092357 | 0.2737072 | 0.9092357 | 0.0000000 | 0.0000007 | 0.0000005 | 6.1577028 | 0.0000000 |
| hsa.miR.93.5p | 3.298589 | 3.328666 | 0.2589551 | 3.398683 | 3.400925 | 0.1891085 | 3.198495 | 3.236571 | 0.2806412 | -0.2001879 | 0.2001879 | 0.6650098 | 0.2001879 | 0.6650098 | 0.0000000 | 0.0000009 | 0.0000006 | 6.0433338 | 0.0000000 |
| hsa.miR.378a.5p | 1.765728 | 1.699123 | 0.3998851 | 1.610886 | 1.612851 | 0.2430057 | 1.920570 | 1.955764 | 0.4624594 | 0.3096836 | -0.3096836 | -1.0287466 | -0.3096836 | -1.0287466 | 0.0000000 | 0.0000011 | 0.0000008 | 5.9662895 | 0.0000000 |
| hsa.miR.146b.5p | 2.601785 | 2.674141 | 0.4626849 | 2.779955 | 2.835954 | 0.2919913 | 2.423615 | 2.450139 | 0.5299317 | -0.3563393 | 0.3563393 | 1.1837335 | 0.3563393 | 1.1837335 | 0.0000000 | 0.0000013 | 0.0000009 | 5.8990220 | 0.0000000 |
| hsa.miR.23a.3p | 3.411765 | 3.464466 | 0.2170216 | 3.494149 | 3.504609 | 0.1702973 | 3.329380 | 3.342163 | 0.2278979 | -0.1647689 | 0.1647689 | 0.5473504 | 0.1647689 | 0.5473504 | 0.0000000 | 0.0000016 | 0.0000011 | 5.7880964 | 0.0000000 |
| hsa.miR.30b.5p | 2.622413 | 2.622930 | 0.3212403 | 2.499914 | 2.507222 | 0.2120817 | 2.744913 | 2.792110 | 0.3634422 | 0.2449988 | -0.2449988 | -0.8138683 | -0.2449988 | -0.8138683 | 0.0000000 | 0.0000017 | 0.0000012 | 5.7695073 | 0.0000000 |
| hsa.miR.625.3p | 2.068354 | 2.104397 | 0.3502308 | 2.200772 | 2.210917 | 0.2188272 | 1.935936 | 1.910435 | 0.4039743 | -0.2648357 | 0.2648357 | 0.8797652 | 0.2648357 | 0.8797652 | 0.0000000 | 0.0000025 | 0.0000017 | 5.6075234 | 0.0000000 |
| hsa.miR.182.5p | 3.674023 | 3.755735 | 0.4922991 | 3.858145 | 3.842168 | 0.3744427 | 3.489902 | 3.616382 | 0.5275933 | -0.3682429 | 0.3682429 | 1.2232765 | 0.3682429 | 1.2232765 | 0.0000000 | 0.0000029 | 0.0000020 | 5.5415728 | 0.0000001 |
| hsa.miR.27a.3p | 3.005903 | 3.044024 | 0.2647920 | 3.104509 | 3.109418 | 0.2287859 | 2.907296 | 2.903005 | 0.2625226 | -0.1972135 | 0.1972135 | 0.6551290 | 0.1972135 | 0.6551290 | 0.0000000 | 0.0000030 | 0.0000020 | 5.5228315 | 0.0000001 |
| hsa.miR.183.5p | 3.203446 | 3.257163 | 0.4833569 | 3.381328 | 3.357706 | 0.3966813 | 3.025563 | 3.143805 | 0.4982314 | -0.3557648 | 0.3557648 | 1.1818251 | 0.3557648 | 1.1818251 | 0.0000000 | 0.0000047 | 0.0000031 | 5.3289624 | 0.0000001 |
| hsa.miR.181c.5p | 1.665600 | 1.682222 | 0.3601516 | 1.795267 | 1.778815 | 0.2462991 | 1.535932 | 1.501756 | 0.4074728 | -0.2593354 | 0.2593354 | 0.8614935 | 0.2593354 | 0.8614935 | 0.0000001 | 0.0000115 | 0.0000076 | 4.9383329 | 0.0000002 |
| hsa.miR.126.3p | 3.305734 | 3.272928 | 0.4223713 | 3.157448 | 3.162873 | 0.2190488 | 3.454020 | 3.630912 | 0.5158520 | 0.2965719 | -0.2965719 | -0.9851906 | -0.2965719 | -0.9851906 | 0.0000002 | 0.0000319 | 0.0000209 | 4.4963337 | 0.0000005 |
| hsa.miR.582.3p | 2.087755 | 2.119436 | 0.3376004 | 1.973266 | 1.974597 | 0.2964765 | 2.202245 | 2.291615 | 0.3386179 | 0.2289783 | -0.2289783 | -0.7606496 | -0.2289783 | -0.7606496 | 0.0000004 | 0.0000584 | 0.0000380 | 4.2335770 | 0.0000010 |
| hsa.miR.143.3p | 4.940749 | 4.860769 | 0.4133211 | 4.799815 | 4.796805 | 0.2682101 | 5.081683 | 4.987285 | 0.4808783 | 0.2818686 | -0.2818686 | -0.9363472 | -0.2818686 | -0.9363472 | 0.0000004 | 0.0000618 | 0.0000398 | 4.2090891 | 0.0000010 |
| hsa.miR.185.5p | 1.698820 | 1.752167 | 0.3122312 | 1.803017 | 1.789962 | 0.1825995 | 1.594623 | 1.585711 | 0.3750133 | -0.2083937 | 0.2083937 | 0.6922687 | 0.2083937 | 0.6922687 | 0.0000007 | 0.0001204 | 0.0000769 | 3.9192525 | 0.0000020 |
| hsa.miR.29c.3p | 3.321214 | 3.327217 | 0.3591607 | 3.202955 | 3.215627 | 0.2277490 | 3.439473 | 3.491354 | 0.4232090 | 0.2365180 | -0.2365180 | -0.7856959 | -0.2365180 | -0.7856959 | 0.0000010 | 0.0001621 | 0.0001026 | 3.7900871 | 0.0000026 |
| hsa.miR.223.3p | 2.257390 | 2.288581 | 0.4632869 | 2.408097 | 2.462940 | 0.4003810 | 2.106684 | 2.111760 | 0.4744849 | -0.3014129 | 0.3014129 | 1.0012719 | 0.3014129 | 1.0012719 | 0.0000011 | 0.0001834 | 0.0001149 | 3.7365180 | 0.0000029 |
| hsa.miR.423.5p | 1.545436 | 1.538957 | 0.3144486 | 1.443133 | 1.425446 | 0.2069216 | 1.647738 | 1.666376 | 0.3670736 | 0.2046048 | -0.2046048 | -0.6796823 | -0.2046048 | -0.6796823 | 0.0000013 | 0.0002154 | 0.0001337 | 3.6667565 | 0.0000034 |
| hsa.miR.151a.5p | 1.778564 | 1.824896 | 0.2355297 | 1.854691 | 1.836098 | 0.1493639 | 1.702436 | 1.739749 | 0.2783202 | -0.1522549 | 0.1522549 | 0.5057800 | 0.1522549 | 0.5057800 | 0.0000016 | 0.0002604 | 0.0001600 | 3.5843739 | 0.0000040 |
| hsa.let.7i.5p | 2.599921 | 2.632392 | 0.2997045 | 2.696086 | 2.717300 | 0.1738861 | 2.503755 | 2.466912 | 0.3627486 | -0.1923305 | 0.1923305 | 0.6389080 | 0.1923305 | 0.6389080 | 0.0000020 | 0.0003296 | 0.0002005 | 3.4820413 | 0.0000050 |
| hsa.miR.26b.5p | 2.777405 | 2.755033 | 0.2942712 | 2.683523 | 2.667076 | 0.2076405 | 2.871288 | 2.871957 | 0.3363026 | 0.1877642 | -0.1877642 | -0.6237392 | -0.1877642 | -0.6237392 | 0.0000020 | 0.0003363 | 0.0002026 | 3.4732893 | 0.0000050 |
| hsa.miR.222.3p | 1.679643 | 1.690400 | 0.3421027 | 1.788188 | 1.797616 | 0.2933599 | 1.571098 | 1.634996 | 0.3540146 | -0.2170897 | 0.2170897 | 0.7211563 | 0.2170897 | 0.7211563 | 0.0000021 | 0.0003468 | 0.0002068 | 3.4599760 | 0.0000051 |
| hsa.miR.320a.3p | 2.517259 | 2.510587 | 0.2335402 | 2.443505 | 2.440882 | 0.2043264 | 2.591012 | 2.575436 | 0.2384649 | 0.1475073 | -0.1475073 | -0.4900086 | -0.1475073 | -0.4900086 | 0.0000023 | 0.0003863 | 0.0002281 | 3.4130330 | 0.0000056 |
| hsa.miR.30e.5p | 3.679150 | 3.640665 | 0.3123538 | 3.579560 | 3.581958 | 0.1513627 | 3.778740 | 3.843580 | 0.3913006 | 0.1991799 | -0.1991799 | -0.6616613 | -0.1991799 | -0.6616613 | 0.0000025 | 0.0004221 | 0.0002467 | 3.3745491 | 0.0000060 |
| hsa.miR.200c.3p | 3.479500 | 3.647500 | 0.6328315 | 3.679499 | 3.713871 | 0.3714689 | 3.279502 | 3.524250 | 0.7654977 | -0.3999973 | 0.3999973 | 1.3287624 | 0.3999973 | 1.3287624 | 0.0000028 | 0.0004717 | 0.0002728 | 3.3263079 | 0.0000066 |
| hsa.miR.145.5p | 3.405874 | 3.362197 | 0.3557557 | 3.294171 | 3.279622 | 0.2492612 | 3.517576 | 3.469948 | 0.4086525 | 0.2234046 | -0.2234046 | -0.7421341 | -0.2234046 | -0.7421341 | 0.0000030 | 0.0004969 | 0.0002844 | 3.3037592 | 0.0000069 |
| hsa.miR.92b.3p | 1.748375 | 1.731752 | 0.3770581 | 1.865526 | 1.808052 | 0.2617419 | 1.631225 | 1.619889 | 0.4352821 | -0.2343014 | 0.2343014 | 0.7783325 | 0.2343014 | 0.7783325 | 0.0000039 | 0.0006400 | 0.0003624 | 3.1938498 | 0.0000088 |
| hsa.miR.629.5p | 1.718671 | 1.767577 | 0.2822432 | 1.804344 | 1.819456 | 0.2016194 | 1.632997 | 1.650836 | 0.3234272 | -0.1713470 | 0.1713470 | 0.5692024 | 0.1713470 | 0.5692024 | 0.0000064 | 0.0010697 | 0.0005993 | 2.9707322 | 0.0000145 |
| hsa.miR.99a.5p | 2.916024 | 2.912899 | 0.3862114 | 2.800660 | 2.801168 | 0.3181101 | 3.031388 | 3.020665 | 0.4143220 | 0.2307282 | -0.2307282 | -0.7664624 | -0.2307282 | -0.7664624 | 0.0000086 | 0.0014262 | 0.0007904 | 2.8458122 | 0.0000190 |
| hsa.miR.22.3p | 4.901288 | 4.935034 | 0.2599745 | 4.979132 | 4.983023 | 0.1344526 | 4.823443 | 4.825832 | 0.3248074 | -0.1556883 | 0.1556883 | 0.5171853 | 0.1556883 | 0.5171853 | 0.0000101 | 0.0016706 | 0.0009158 | 2.7771206 | 0.0000220 |
| hsa.miR.10b.5p | 4.284825 | 4.160990 | 0.6577961 | 4.092498 | 4.126032 | 0.2208435 | 4.477153 | 4.339191 | 0.8637267 | 0.3846552 | -0.3846552 | -1.2777969 | -0.3846552 | -1.2777969 | 0.0000184 | 0.0030501 | 0.0016537 | 2.5156825 | 0.0000396 |
| hsa.miR.142.3p | 2.908082 | 2.993345 | 0.5523317 | 3.062898 | 3.069081 | 0.3324835 | 2.753266 | 2.754739 | 0.6738583 | -0.3096321 | 0.3096321 | 1.0285755 | 0.3096321 | 1.0285755 | 0.0000350 | 0.0058148 | 0.0031176 | 2.2354673 | 0.0000745 |
| hsa.miR.16.5p | 2.418426 | 2.396977 | 0.2678058 | 2.344887 | 2.354009 | 0.1520643 | 2.491965 | 2.532161 | 0.3317754 | 0.1470782 | -0.1470782 | -0.4885833 | -0.1470782 | -0.4885833 | 0.0000518 | 0.0086050 | 0.0045617 | 2.0652508 | 0.0001089 |
| hsa.miR.10a.5p | 4.453193 | 4.572159 | 0.4172756 | 4.567356 | 4.619375 | 0.2726925 | 4.339031 | 4.448143 | 0.4992066 | -0.2283251 | 0.2283251 | 0.7584795 | 0.2283251 | 0.7584795 | 0.0000528 | 0.0087721 | 0.0045974 | 2.0568959 | 0.0001097 |
| hsa.miR.365a.3p | 1.558982 | 1.524607 | 0.3288053 | 1.472455 | 1.482687 | 0.2603646 | 1.645509 | 1.646930 | 0.3665257 | 0.1730535 | -0.1730535 | -0.5748714 | -0.1730535 | -0.5748714 | 0.0000972 | 0.0161318 | 0.0083574 | 1.7923179 | 0.0001970 |
| hsa.miR.365b.3p | 1.559072 | 1.524607 | 0.3286232 | 1.472600 | 1.482687 | 0.2598729 | 1.645545 | 1.646930 | 0.3665720 | 0.1729456 | -0.1729456 | -0.5745130 | -0.1729456 | -0.5745130 | 0.0000973 | 0.0161562 | 0.0083574 | 1.7916615 | 0.0001970 |
| hsa.miR.20a.5p | 2.167170 | 2.188072 | 0.3531756 | 2.258504 | 2.252491 | 0.2151305 | 2.075836 | 2.092815 | 0.4330362 | -0.1826683 | 0.1826683 | 0.6068109 | 0.1826683 | 0.6068109 | 0.0001387 | 0.0230266 | 0.0116520 | 1.6377698 | 0.0002774 |
| hsa.miR.195.5p | 1.610326 | 1.644712 | 0.4593292 | 1.492892 | 1.530241 | 0.2351047 | 1.727760 | 1.829698 | 0.5838159 | 0.2348685 | -0.2348685 | -0.7802161 | -0.2348685 | -0.7802161 | 0.0001727 | 0.0286635 | 0.0143318 | 1.5426701 | 0.0003412 |
| hsa.miR.26a.5p | 3.363368 | 3.336961 | 0.2249507 | 3.307628 | 3.297116 | 0.1471895 | 3.419108 | 3.407502 | 0.2715615 | 0.1114806 | -0.1114806 | -0.3703306 | -0.1114806 | -0.3703306 | 0.0002606 | 0.0432635 | 0.0213711 | 1.3638783 | 0.0005090 |
| hsa.miR.145.3p | 1.779374 | 1.754841 | 0.2975307 | 1.706504 | 1.693139 | 0.2239980 | 1.852244 | 1.840403 | 0.3420364 | 0.1457395 | -0.1457395 | -0.4841363 | -0.1457395 | -0.4841363 | 0.0002988 | 0.0495960 | 0.0242005 | 1.3045533 | 0.0005767 |
| hsa.miR.142.5p | 1.517108 | 1.642632 | 0.7709832 | 1.707036 | 1.728336 | 0.3336782 | 1.327180 | 1.413437 | 1.0051222 | -0.3798562 | 0.3798562 | 1.2618548 | 0.3798562 | 1.2618548 | 0.0003066 | 0.0509030 | 0.0245316 | 1.2932569 | 0.0005851 |
| hsa.miR.155.5p | 2.133480 | 2.195366 | 0.4195203 | 2.233687 | 2.297068 | 0.3475670 | 2.033272 | 2.006969 | 0.4610634 | -0.2004154 | 0.2004154 | 0.6657657 | 0.2004154 | 0.6657657 | 0.0004167 | 0.0691679 | 0.0329172 | 1.1600957 | 0.0007860 |
| hsa.let.7d.5p | 2.204108 | 2.185887 | 0.2122742 | 2.154807 | 2.147458 | 0.1420691 | 2.253409 | 2.269843 | 0.2558420 | 0.0986016 | -0.0986016 | -0.3275473 | -0.0986016 | -0.3275473 | 0.0006292 | 0.1044446 | 0.0490764 | 0.9811142 | 0.0011735 |
| hsa.miR.101.3p | 4.064812 | 4.041831 | 0.3932389 | 3.975163 | 3.934040 | 0.1680979 | 4.154461 | 4.258030 | 0.5159943 | 0.1792983 | -0.1792983 | -0.5956161 | -0.1792983 | -0.5956161 | 0.0008471 | 0.1406149 | 0.0652250 | 0.8519688 | 0.0015624 |
| hsa.miR.15a.5p | 1.962872 | 1.985385 | 0.2869339 | 2.027709 | 2.007988 | 0.1768348 | 1.898034 | 1.940992 | 0.3545154 | -0.1296752 | 0.1296752 | 0.4307717 | 0.1296752 | 0.4307717 | 0.0008984 | 0.1491266 | 0.0678151 | 0.8264448 | 0.0016209 |
| hsa.miR.140.3p | 3.000561 | 3.018035 | 0.2271711 | 2.949429 | 2.935298 | 0.2005767 | 3.051693 | 3.090265 | 0.2412282 | 0.1022638 | -0.1022638 | -0.3397129 | -0.1022638 | -0.3397129 | 0.0008923 | 0.1481224 | 0.0678151 | 0.8293794 | 0.0016209 |
| hsa.miR.193a.5p | 2.336431 | 2.300347 | 0.3276854 | 2.266929 | 2.278125 | 0.1938504 | 2.405932 | 2.378371 | 0.4104126 | 0.1390021 | -0.1390021 | -0.4617551 | -0.1390021 | -0.4617551 | 0.0018588 | 0.3085666 | 0.1375538 | 0.5106511 | 0.0033179 |
| hsa.let.7b.5p | 4.195831 | 4.209035 | 0.2924159 | 4.256938 | 4.282751 | 0.1889508 | 4.134724 | 4.104211 | 0.3585804 | -0.1222138 | 0.1222138 | 0.4059855 | 0.1222138 | 0.4059855 | 0.0021512 | 0.3570954 | 0.1570359 | 0.4472157 | 0.0037989 |
| hsa.miR.425.5p | 1.923042 | 1.930834 | 0.3243793 | 1.987356 | 1.978949 | 0.2395357 | 1.858729 | 1.880977 | 0.3817182 | -0.1286263 | 0.1286263 | 0.4272874 | 0.1286263 | 0.4272874 | 0.0035774 | 0.5938450 | 0.2575713 | 0.2263269 | 0.0062510 |
| hsa.miR.99b.5p | 4.315202 | 4.300285 | 0.2601134 | 4.263737 | 4.282048 | 0.1951765 | 4.366667 | 4.343604 | 0.3041630 | 0.1029303 | -0.1029303 | -0.3419271 | -0.1029303 | -0.3419271 | 0.0036421 | 0.6045962 | 0.2585923 | 0.2185346 | 0.0062979 |
| hsa.miR.146b.3p | 1.886946 | 1.965307 | 0.4754291 | 1.979342 | 1.993235 | 0.3044790 | 1.794549 | 1.860622 | 0.5867326 | -0.1847929 | 0.1847929 | 0.6138687 | 0.1847929 | 0.6138687 | 0.0043674 | 0.7249845 | 0.3057163 | 0.1396713 | 0.0074741 |
| hsa.miR.128.3p | 1.955925 | 1.943604 | 0.2304255 | 2.000480 | 1.993252 | 0.1994596 | 1.911370 | 1.897153 | 0.2508004 | -0.0891101 | 0.0891101 | 0.2960174 | 0.0891101 | 0.2960174 | 0.0044531 | 0.7392212 | 0.3072666 | 0.1312256 | 0.0075431 |
| hsa.miR.34a.5p | 2.074666 | 2.121651 | 0.2675331 | 2.125712 | 2.136585 | 0.1931050 | 2.023620 | 2.059319 | 0.3182343 | -0.1020923 | 0.1020923 | 0.3391431 | 0.1020923 | 0.3391431 | 0.0050922 | 0.8453067 | 0.3462702 | 0.0729857 | 0.0085385 |
| hsa.miR.1307.5p | 2.032668 | 2.074195 | 0.4746939 | 2.121558 | 2.143052 | 0.3137240 | 1.943777 | 1.930948 | 0.5817384 | -0.1777808 | 0.1777808 | 0.5905749 | 0.1777808 | 0.5905749 | 0.0060341 | 1.0000000 | 0.4042856 | 0.0000000 | 0.0100166 |
| hsa.miR.146a.5p | 1.834930 | 1.878293 | 0.5428638 | 1.936147 | 1.968467 | 0.3763981 | 1.733712 | 1.804289 | 0.6556095 | -0.2024345 | 0.2024345 | 0.6724729 | 0.2024345 | 0.6724729 | 0.0062340 | 1.0000000 | 0.4114442 | 0.0000000 | 0.0102460 |
| hsa.miR.660.5p | 1.637156 | 1.706445 | 0.5648980 | 1.742335 | 1.736172 | 0.1929619 | 1.531977 | 1.656099 | 0.7626676 | -0.2103579 | 0.2103579 | 0.6987938 | 0.2103579 | 0.6987938 | 0.0065781 | 1.0000000 | 0.4275745 | 0.0000000 | 0.0107055 |
| hsa.miR.1307.3p | 2.668366 | 2.682073 | 0.3103661 | 2.725068 | 2.712113 | 0.1957961 | 2.611663 | 2.652759 | 0.3856627 | -0.1134058 | 0.1134058 | 0.3767259 | 0.1134058 | 0.3767259 | 0.0074280 | 1.0000000 | 0.4753900 | 0.0000000 | 0.0119713 |
| hsa.miR.17.3p | 2.280466 | 2.310070 | 0.2760079 | 2.330198 | 2.324300 | 0.1630184 | 2.230733 | 2.251456 | 0.3485844 | -0.0994646 | 0.0994646 | 0.3304142 | 0.0994646 | 0.3304142 | 0.0083333 | 1.0000000 | 0.5249975 | 0.0000000 | 0.0133012 |
| hsa.miR.103a.3p | 4.078473 | 4.104653 | 0.2058716 | 4.115271 | 4.122395 | 0.1680536 | 4.041675 | 4.049734 | 0.2327882 | -0.0735962 | 0.0735962 | 0.2444812 | 0.0735962 | 0.2444812 | 0.0086789 | 1.0000000 | 0.5380907 | 0.0000000 | 0.0137209 |
| hsa.miR.484 | 1.597652 | 1.580193 | 0.2719205 | 1.550795 | 1.553409 | 0.1598979 | 1.644510 | 1.656175 | 0.3443530 | 0.0937157 | -0.0937157 | -0.3113168 | -0.0937157 | -0.3113168 | 0.0116710 | 1.0000000 | 0.7119329 | 0.0000000 | 0.0182773 |
| hsa.miR.452.5p | 1.609759 | 1.684291 | 0.4772755 | 1.691423 | 1.719895 | 0.2895699 | 1.528095 | 1.619481 | 0.6003483 | -0.1633282 | 0.1633282 | 0.5425647 | 0.1633282 | 0.5425647 | 0.0122598 | 1.0000000 | 0.7355852 | 0.0000000 | 0.0189271 |
| hsa.miR.584.5p | 1.562512 | 1.609699 | 0.4055066 | 1.631695 | 1.617142 | 0.3258710 | 1.493330 | 1.570896 | 0.4632148 | -0.1383646 | 0.1383646 | 0.4596372 | 0.1383646 | 0.4596372 | 0.0123140 | 1.0000000 | 0.7355852 | 0.0000000 | 0.0189271 |
| hsa.miR.9.5p | 2.452682 | 2.417320 | 0.5298502 | 2.364790 | 2.362214 | 0.3600516 | 2.540574 | 2.612118 | 0.6472233 | 0.1757844 | -0.1757844 | -0.5839430 | -0.1757844 | -0.5839430 | 0.0151165 | 1.0000000 | 0.8767577 | 0.0000000 | 0.0230215 |
| hsa.miR.361.3p | 2.114070 | 2.138671 | 0.2668813 | 2.157051 | 2.182644 | 0.1719882 | 2.071090 | 2.091288 | 0.3313815 | -0.0859613 | 0.0859613 | 0.2855574 | 0.0859613 | 0.2855574 | 0.0184170 | 1.0000000 | 1.0000000 | 0.0000000 | 0.0277930 |
| hsa.let.7g.5p | 2.743360 | 2.731598 | 0.2633678 | 2.701240 | 2.687710 | 0.2007329 | 2.785480 | 2.824734 | 0.3090374 | 0.0842401 | -0.0842401 | -0.2798397 | -0.0842401 | -0.2798397 | 0.0191012 | 1.0000000 | 1.0000000 | 0.0000000 | 0.0285658 |
| hsa.let.7a.3p | 1.362918 | 1.456311 | 0.5840349 | 1.454096 | 1.472496 | 0.2172292 | 1.271740 | 1.413722 | 0.7883141 | -0.1823566 | 0.1823566 | 0.6057754 | 0.1823566 | 0.6057754 | 0.0227488 | 1.0000000 | 1.0000000 | 0.0000000 | 0.0337170 |
| hsa.miR.28.3p | 3.478699 | 3.452430 | 0.2371295 | 3.442283 | 3.445475 | 0.2164372 | 3.515115 | 3.488616 | 0.2519303 | 0.0728325 | -0.0728325 | -0.2419443 | -0.0728325 | -0.2419443 | 0.0243409 | 1.0000000 | 1.0000000 | 0.0000000 | 0.0355939 |
| hsa.miR.23b.3p | 3.145549 | 3.139008 | 0.1654088 | 3.120156 | 3.106189 | 0.1396735 | 3.170942 | 3.185124 | 0.1848453 | 0.0507862 | -0.0507862 | -0.1687082 | -0.0507862 | -0.1687082 | 0.0244440 | 1.0000000 | 1.0000000 | 0.0000000 | 0.0355939 |
| hsa.miR.29b.3p | 2.730065 | 2.739194 | 0.3702233 | 2.785646 | 2.771371 | 0.2357865 | 2.674484 | 2.713670 | 0.4621597 | -0.1111620 | 0.1111620 | 0.3692721 | 0.1111620 | 0.3692721 | 0.0281053 | 1.0000000 | 1.0000000 | 0.0000000 | 0.0405694 |
Let’s visualize the results of differential expression using heatmap and vulcano plot.
ks.heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = F, margins = c(10, 10))
Z-scoring the values before clustering and plotting will help us to gain more insight.
ks.heatmap(x = dplyr::select(trainx, sig_de$miR), rlab = data.frame(Class = train$Class), zscore = T, margins = c(10, 10))
We will also create a vulcano plot and label top 10 most significant miRNAs:
ks.vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = sig_de$miR[1:10])
We may also what to check the consistency of differential expression between datasets:
de_test = ks.miRNA_differential_expression(dplyr::select(test, starts_with("hsa")), test$Class)
de_valid = ks.miRNA_differential_expression(dplyr::select(valid, starts_with("hsa")), valid$Class)
ks.correlation_plot(de$log2FC, de_test$log2FC, "log2FC on training set", "log2FC on test set", "", yx = T)
ks.correlation_plot(de$log2FC, de_valid$log2FC, "log2FC on training set", "log2FC on validation set", "", yx = T)
ks.correlation_plot(de_test$log2FC, de_valid$log2FC, "log2FC on test set", "log2FC on validation set", "", yx = T)
5 miRNA selection
The main feature of this package is the shotgun-like feature selection evaluation of possible miRNA signatures of biological processes. The function can be applied in a straightforward way, e.g.:
selected_features = ks.miRNAselector(wd = getwd(), m = c(1:4), max_iterations = 1, stamp = "tutorial") # For the sake of this tutorial and vignette building we will use only few fastest methods. The m parameter defines what methods will be tested. See more details below.But, for largers projects we suggest using the following wrapper wich will perform the feature selection in parallel, significantly reducing computational time. We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing:
readLines("Tutorial_miRNAselector.R") %>% paste0(collapse = "\n") %>% cat
#> #options(warn = -1)
#> suppressMessages(library(foreach))
#> suppressMessages(library(doParallel))
#> suppressMessages(library(parallel))
#> suppressMessages(library(doSNOW))
#>
#> m = 1:56 # which methods to check?
#>
#> cl <- makeCluster(5) # We do not recommend using more than 5 threads, beacuse some of the methods inhereditly use multicore processing.
#> doSNOW::registerDoSNOW(cl)
#> iterations = length(m)
#> pb <- txtProgressBar(max = iterations, style = 3)
#> progress <- function(n) setTxtProgressBar(pb, n)
#> opts <- list(progress = progress)
#> foreach(i = m, .options.snow = opts) %dopar%
#> {
#> suppressMessages(library(miRNAselector))
#> # setwd("/miRNAselector/miRNAselector/vignettes") # change it you to your working directory
#> ks.miRNAselector(m = i, max_iterations = 1, stamp = "tutorial", debug = F, # we set debug to false (to make the package smaller), you may also want to change stamp to something meaningful, max_iterations was set to 1 to recude the computational time.. in real life scenarios it is resonable to use at least 10 iterations.
#> prefer_no_features = 11, # Few methods are filter rather than wrapper methods, thus requires the maximum number of maximum features.
#> conda_path = "/opt/conda/bin/conda", # Methods line WxNet requires usage of python. In setup script we create conda enviorment. Providing conda_path makes it easier to activate env. We prefer this apporach over use_condaenv.
#> timeout = 600) # We don't want to wait eternity in this tutorial, just 10 minutes. Timeout is useful for complicated methods. Depending on your CPU 2 days may be reasonable for larger projects. Note that some methods cannot be controled with timeout parameter.
#> }
#>
#> stopCluster(cl)
#> #options(warn = 0)A few notes about what is does:
- This function iterates though available methods which are described by
mparameter. The aim of this function is to perform feature selection using multiple methods and to create formulas for benchmarking. - It loads the data from working directory. The output is mainly put in files in the working directory. Log and temporary files are placed in a created
tempsubfolder.
Files created for each method (e.g. for stamp=tutorial and m=1):
formulastutorial-1.RDS- main result file containing the final formula (final set of miRNAs selected by this method).time1-formula.RDS- time taken to compute the resultstutorial1featureselection.log- log file of the process- (optional)
all1-tutorial.rdata- all variables created during feature selection (created ifdebug=T).
Pearls about the methods:
Sig= miRNAs with p-value <0.05 after BH correction (DE using t-test)Fcsig=sig+ absolute log2FC filter (included if abs. log2FC>1)Cfs= Correlation-based Feature Selection for Machine Learning (more: https://www.cs.waikato.ac.nz/~mhall/thesis.pdf)Classloop= Classification using different classification algorithms (classifiers) with the embedded feature selection and using the different schemes for the performance validation (more: https://rdrr.io/cran/Biocomb/man/classifier.loop.html)Fcfs= CFS algorithm with forward search (https://rdrr.io/cran/Biocomb/man/select.forward.Corr.html)MDLmethods = minimal description length (MDL) discretization algorithm with different a method of feature ranking or feature selection (AUC, SU, CorrSF) (more: https://rdrr.io/cran/Biocomb/man/select.process.html)bounceR= genetic algorithm with componentwise boosting (more: https://www.statworx.com/ch/blog/automated-feature-selection-using-bouncer/)RandomForestRFE= recursive feature elimination using random forest with resampling to assess the performance. (more: https://topepo.github.io/caret/recursive-feature-elimination.html#resampling-and-external-validation)GeneticAlgorithmRF(more: https://topepo.github.io/caret/feature-selection-using-genetic-algorithms.html)SimulatedAnnealing= makes small random changes (i.e. perturbations) to an initial candidate solution (more: https://topepo.github.io/caret/feature-selection-using-simulated-annealing.html)Boruta(more: https://www.jstatsoft.org/article/view/v036i11/v36i11.pdf)spFSR= simultaneous perturbation stochastic approximation (SPSA-FSR) (more: https://arxiv.org/abs/1804.05589)varSelRF= using the out-of-bag error as minimization criterion, carry out variable elimination from random forest, by successively eliminating the least important variables (with importance as returned from random forest). (more: https://www.ncbi.nlm.nih.gov/pubmed/16398926)WxNet= a neural network-based feature selection algorithm for transcriptomic data (more: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642261/)Step= backward stepwise method of feature selection based on logistic regression (GLM, family = binomial) using AIC criteria (stepAIC) and functions from My.stepwise package (https://cran.r-project.org/web/packages/My.stepwise/index.html)
Notes about methods:
Comming soon…
The miRNAselector functions saves all output files to temp/ directory. As users may want to run multiple selection methods in different configurations, we do not recommend using the return of this function in the following steps. Instead, we provide ks.merge_formulas() which conviniently summerizes the results of feature selection. We can do:
selected_sets_of_miRNAs = ks.merge_formulas(max_miRNAs = 11) # we filter out sets with more than 11 miRNAs.
selected_sets_of_miRNAs_with_own = ks.merge_formulas(max_miRNAs = 11, add = list(my_own_signature = c("hsa.miR.192.5p", "hsa.let.7g.5p", "hsa.let.7a.5p",
"hsa.let.7d.5p", "hsa.miR.194.5p", "hsa.miR.98.5p", "hsa.let.7f.5p", "hsa.miR.26b.5p"))) # you can also add your own signature (for example selected from literature)Note that:
- Two files are created in working directory: (1)
featureselection_formulas_all.RDS- contains the formulas for all selection methods, (2)featureselection_formulas_final.RDS- contains methods that selected smaller or equal number of microRNAs than specified inmax_miRNAparameter, as well asfcsigandcfs_sig. - The results of
fcsigandcfs_sigmethods are always retained in the finalformulasset (ignoringmax_miRNAparameter) - they are commonly used as benchmark comparator for the final set of miRNAs. Those sets can be manually removed (if needed) from final selection. - Readable tables are written in corresponding
*.csvfiles.
Let’s analyze the process of feature selection:
all_sets = readRDS("featureselection_formulas_all.RDS")
length(all_sets) # How many feature selection methods completed in time?
#> [1] 17
final_sets = readRDS("featureselection_formulas_final.RDS")
length(final_sets) # How many feature selection methods completed in time and fulfilled max_miRNA criteria? (remember about fcsig and cfs_sig)
#> [1] 13
featureselection_formulas_final = fread("featureselection_formulas_final.csv")
ks.table(featureselection_formulas_final) # show information about selected formulas| name | formula | ile_miRNA |
|---|---|---|
| cfs_sig | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p | 34 |
| fcsig | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p | 50 |
| my_own_signature | Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p | 0 |
| sigtop | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p | 11 |
| sigtopBonf | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p | 11 |
| sigtopHolm | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p | 11 |
| topFC | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p | 11 |
| sigtopSMOTE | Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p | 11 |
| sigtopBonfSMOTE | Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p | 11 |
| sigtopHolmSMOTE | Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p | 11 |
| topFCSMOTE | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p | 11 |
| cfsSMOTE | Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p | 5 |
| cfsSMOTE_sig | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p | 5 |
Note that my_own_signture has 0 miRNAs according to the table. This trick is done to make sure that signatures added manually will not be filtered out based on max_miRNA parameter.
Now, we will summarize number of microRNAs selected by methods implemented in ks.miRNAselector by creating histogram and calculating some descriptive statistics.
hist(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)], breaks = ncol(train), main = "Number of selected microRNAs distribution",
xlab = "Number of selected microRNAs") # Histogram showing how many miRNAs were selected in final set.
psych::describe(featureselection_formulas_final$ile_miRNA[-which(featureselection_formulas_final$ile_miRNA == 0)]) # Descriptive statistics of how many features where selected in the final set.
#> vars n mean sd median trimmed mad min max range skew kurtosis se
#> X1 1 12 15.17 13.19 11 12.7 0 5 50 45 1.68 1.47 3.816 Benchmarking
In the next step of looking for the best microRNA signature, we perform benchmarking. This tests all the signatures using different classifier architectures. Here is the example of benchmark with default parameters:
readLines("Tutorial_benchmark.R") %>% paste0(collapse = "\n") %>% catJust for rendering this tutorial we will use a very simple benchmark using only logistic regression and conditional trees.
ks.benchmark(search_iters = 5, # 5 random hyperparameter sets will be checked; 5 is set here for speed purposes.. for real projects use more, like 5000...
algorithms = c("ctree"), # just add ctree, note that logistic regression (glm) is always included
output_file = paste0("benchmark.csv")) # the main output
#> method SMOTE
#> 1 cfs_sig No
#> 2 fcsig No
#> 3 my_own_signature No
#> 4 sigtop No
#> 5 sigtopBonf No
#> 6 sigtopHolm No
#> 7 topFC No
#> 8 sigtopSMOTE Yes
#> 9 sigtopBonfSMOTE Yes
#> 10 sigtopHolmSMOTE Yes
#> 11 topFCSMOTE Yes
#> 12 cfsSMOTE Yes
#> 13 cfsSMOTE_sig Yes
#> miRy
#> 1 Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + \n hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p
#> 2 Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + \n hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p
#> 3 Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p
#> 4 Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 5 Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 6 Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p
#> 7 Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p
#> 8 Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 9 Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 10 Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p
#> 11 Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p
#> 12 Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p
#> 13 Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p
#> glm_modelname glm_train_ROCAUC glm_train_ROCAUC_lower95CI
#> 1 1589555030 1.0000000 1
#> 2 1589555038 1.0000000 1
#> 3 1589555046 0.9239235 0.890138639558989
#> 4 1589555053 0.9961569 0.990219096927101
#> 5 1589555061 0.9961569 0.990219096927101
#> 6 1589555069 0.9961569 0.990219096927101
#> 7 1589555076 0.9939733 0.985662071431939
#> 8 1589555086 0.9959498 0.995452486604309
#> 9 1589555105 0.9959498 0.995452486604309
#> 10 1589555124 0.9959498 0.995452486604309
#> 11 1589555144 0.9980369 0.997607014342334
#> 12 1589555162 0.9978472 0.997284443457432
#> 13 1589555179 0.9978472 0.997284443457432
#> glm_train_ROCAUC_upper95CI glm_train_Accuracy glm_train_Sensitivity
#> 1 1 1.0000000 1.0000000
#> 2 1 1.0000000 1.0000000
#> 3 0.957708333975817 0.8317757 0.8504673
#> 4 1 0.9859813 1.0000000
#> 5 1 0.9859813 1.0000000
#> 6 1 0.9859813 1.0000000
#> 7 1 0.9813084 0.9906542
#> 8 0.996447190742236 0.9788441 0.9814019
#> 9 0.996447190742236 0.9788441 0.9814019
#> 10 0.996447190742236 0.9788441 0.9814019
#> 11 0.998466748855455 0.9929325 1.0000000
#> 12 0.998409884120141 0.9845167 0.9801869
#> 13 0.998409884120141 0.9845167 0.9801869
#> glm_train_Specificity glm_test_Accuracy glm_test_Sensitivity
#> 1 1.0000000 0.8888889 0.9166667
#> 2 1.0000000 0.9166667 0.9166667
#> 3 0.8130841 0.8472222 0.8055556
#> 4 0.9719626 0.9444444 1.0000000
#> 5 0.9719626 0.9444444 1.0000000
#> 6 0.9719626 0.9444444 1.0000000
#> 7 0.9719626 0.9444444 1.0000000
#> 8 0.9763116 0.8888889 0.9166667
#> 9 0.9763116 0.8888889 0.9166667
#> 10 0.9763116 0.8888889 0.9166667
#> 11 0.9859350 0.9583333 1.0000000
#> 12 0.9888036 0.9305556 0.9722222
#> 13 0.9888036 0.9305556 0.9722222
#> glm_test_Specificity glm_valid_Accuracy glm_valid_Sensitivity
#> 1 0.8611111 1.0000000 1.0000000
#> 2 0.9166667 0.9571429 1.0000000
#> 3 0.8888889 0.8857143 0.8857143
#> 4 0.8888889 0.9714286 1.0000000
#> 5 0.8888889 0.9714286 1.0000000
#> 6 0.8888889 0.9714286 1.0000000
#> 7 0.8888889 0.9857143 1.0000000
#> 8 0.8611111 0.9714286 1.0000000
#> 9 0.8611111 0.9714286 1.0000000
#> 10 0.8611111 0.9714286 1.0000000
#> 11 0.9166667 0.9857143 1.0000000
#> 12 0.8888889 0.9857143 1.0000000
#> 13 0.8888889 0.9857143 1.0000000
#> glm_valid_Specificity ctree_modelname ctree_train_ROCAUC
#> 1 1.0000000 1589555213 0.9768539
#> 2 0.9142857 1589555220 0.9943663
#> 3 0.8857143 1589555229 0.9753254
#> 4 0.9428571 1589555236 0.9905232
#> 5 0.9428571 1589555244 0.9905232
#> 6 0.9428571 1589555252 0.9905232
#> 7 0.9714286 1589555260 0.9944537
#> 8 0.9428571 1589555269 0.9999317
#> 9 0.9428571 1589555288 0.9999317
#> 10 0.9428571 1589555306 0.9999317
#> 11 0.9714286 1589555325 0.9998280
#> 12 0.9714286 1589555343 0.9997226
#> 13 0.9714286 1589555360 0.9997226
#> ctree_train_ROCAUC_lower95CI ctree_train_ROCAUC_upper95CI
#> 1 0.956749862266401 0.996957885135119
#> 2 0.989250362911224 0.999482277494052
#> 3 0.960566402099731 0.990084309752833
#> 4 0.979470550029621 1
#> 5 0.979470550029621 1
#> 6 0.979470550029621 1
#> 7 0.989338017532758 0.999569310618172
#> 8 0.999862825420904 1
#> 9 0.999862825420904 1
#> 10 0.999862825420904 1
#> 11 0.999683105091608 0.999972993542974
#> 12 0.999601917343718 0.999843371232655
#> 13 0.999601917343718 0.999843371232655
#> ctree_train_Accuracy ctree_train_Sensitivity ctree_train_Specificity
#> 1 0.9485981 0.9813084 0.9158879
#> 2 0.9579439 0.9345794 0.9813084
#> 3 0.8971963 0.8317757 0.9626168
#> 4 0.9579439 0.9345794 0.9813084
#> 5 0.9579439 0.9345794 0.9813084
#> 6 0.9579439 0.9345794 0.9813084
#> 7 0.9579439 0.9906542 0.9252336
#> 8 0.9989771 1.0000000 0.9979643
#> 9 0.9989771 1.0000000 0.9979643
#> 10 0.9989771 1.0000000 0.9979643
#> 11 0.9992096 1.0000000 0.9984269
#> 12 0.9986051 1.0000000 0.9972240
#> 13 0.9986051 1.0000000 0.9972240
#> ctree_test_Accuracy ctree_test_Sensitivity ctree_test_Specificity
#> 1 0.9305556 1.0000000 0.8611111
#> 2 0.9166667 0.9444444 0.8888889
#> 3 0.7916667 0.6944444 0.8888889
#> 4 0.9166667 0.9444444 0.8888889
#> 5 0.9166667 0.9444444 0.8888889
#> 6 0.9166667 0.9444444 0.8888889
#> 7 0.9305556 0.9722222 0.8888889
#> 8 0.9305556 0.8888889 0.9722222
#> 9 0.9305556 0.8888889 0.9722222
#> 10 0.9305556 0.8888889 0.9722222
#> 11 0.9583333 0.9166667 1.0000000
#> 12 0.9444444 0.9444444 0.9444444
#> 13 0.9444444 0.9444444 0.9444444
#> ctree_valid_Accuracy ctree_valid_Sensitivity ctree_valid_Specificity
#> 1 0.9571429 1.0000000 0.9142857
#> 2 0.9571429 0.9714286 0.9428571
#> 3 0.8714286 0.8000000 0.9428571
#> 4 0.9571429 0.9714286 0.9428571
#> 5 0.9571429 0.9714286 0.9428571
#> 6 0.9571429 0.9714286 0.9428571
#> 7 0.9714286 1.0000000 0.9428571
#> 8 0.9428571 0.8857143 1.0000000
#> 9 0.9428571 0.8857143 1.0000000
#> 10 0.9428571 0.8857143 1.0000000
#> 11 0.9142857 0.8285714 1.0000000
#> 12 0.9571429 0.9428571 0.9714286
#> 13 0.9571429 0.9428571 0.9714286As benchmarking is done, the main result file is saved in file specified in output_file parameter. It contains the performance metrics of signatures satisfying initial criteria (e.g. max_miRNA) across different methods of modelling. Let’s take a quick look:
ks.table(fread("benchmark.csv"))| V1 | method | SMOTE | miRy | glm_modelname | glm_train_ROCAUC | glm_train_ROCAUC_lower95CI | glm_train_ROCAUC_upper95CI | glm_train_Accuracy | glm_train_Sensitivity | glm_train_Specificity | glm_test_Accuracy | glm_test_Sensitivity | glm_test_Specificity | glm_valid_Accuracy | glm_valid_Sensitivity | glm_valid_Specificity | ctree_modelname | ctree_train_ROCAUC | ctree_train_ROCAUC_lower95CI | ctree_train_ROCAUC_upper95CI | ctree_train_Accuracy | ctree_train_Sensitivity | ctree_train_Specificity | ctree_test_Accuracy | ctree_test_Sensitivity | ctree_test_Specificity | ctree_valid_Accuracy | ctree_valid_Sensitivity | ctree_valid_Specificity |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | cfs_sig | No | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p | 1589555030 | 1.0000000 | 1.0000000 | 1.0000000 | 1.0000000 | 1.0000000 | 1.0000000 | 0.8888889 | 0.9166667 | 0.8611111 | 1.0000000 | 1.0000000 | 1.0000000 | 1589555213 | 0.9768539 | 0.9567499 | 0.9969579 | 0.9485981 | 0.9813084 | 0.9158879 | 0.9305556 | 1.0000000 | 0.8611111 | 0.9571429 | 1.0000000 | 0.9142857 |
| 2 | fcsig | No | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.127.5p + hsa.miR.381.3p + hsa.miR.127.3p + hsa.miR.199a.3p + hsa.miR.181b.5p + hsa.miR.199b.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.30a.5p + hsa.miR.200a.5p + hsa.miR.136.5p + hsa.miR.192.5p + hsa.miR.451a + hsa.miR.200a.3p + hsa.miR.141.3p + hsa.miR.200b.3p + hsa.miR.708.3p + hsa.miR.210.3p + hsa.miR.486.5p + hsa.miR.378a.3p + hsa.miR.379.5p + hsa.miR.141.5p + hsa.miR.21.3p + hsa.miR.337.3p + hsa.miR.144.5p + hsa.miR.429 + hsa.miR.335.3p + hsa.miR.126.5p + hsa.miR.181a.3p + hsa.miR.181a.5p + hsa.miR.378a.5p + hsa.miR.146b.5p + hsa.miR.182.5p + hsa.miR.183.5p + hsa.miR.223.3p + hsa.miR.200c.3p + hsa.miR.10b.5p + hsa.miR.142.3p + hsa.miR.142.5p | 1589555038 | 1.0000000 | 1.0000000 | 1.0000000 | 1.0000000 | 1.0000000 | 1.0000000 | 0.9166667 | 0.9166667 | 0.9166667 | 0.9571429 | 1.0000000 | 0.9142857 | 1589555220 | 0.9943663 | 0.9892504 | 0.9994823 | 0.9579439 | 0.9345794 | 0.9813084 | 0.9166667 | 0.9444444 | 0.8888889 | 0.9571429 | 0.9714286 | 0.9428571 |
| 3 | my_own_signature | No | Class ~ hsa.miR.192.5p + hsa.let.7g.5p + hsa.let.7a.5p + hsa.let.7d.5p + hsa.miR.194.5p + hsa.miR.98.5p + hsa.let.7f.5p + hsa.miR.26b.5p | 1589555046 | 0.9239235 | 0.8901386 | 0.9577083 | 0.8317757 | 0.8504673 | 0.8130841 | 0.8472222 | 0.8055556 | 0.8888889 | 0.8857143 | 0.8857143 | 0.8857143 | 1589555229 | 0.9753254 | 0.9605664 | 0.9900843 | 0.8971963 | 0.8317757 | 0.9626168 | 0.7916667 | 0.6944444 | 0.8888889 | 0.8714286 | 0.8000000 | 0.9428571 |
| 4 | sigtop | No | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p | 1589555053 | 0.9961569 | 0.9902191 | 1.0000000 | 0.9859813 | 1.0000000 | 0.9719626 | 0.9444444 | 1.0000000 | 0.8888889 | 0.9714286 | 1.0000000 | 0.9428571 | 1589555236 | 0.9905232 | 0.9794706 | 1.0000000 | 0.9579439 | 0.9345794 | 0.9813084 | 0.9166667 | 0.9444444 | 0.8888889 | 0.9571429 | 0.9714286 | 0.9428571 |
| 5 | sigtopBonf | No | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p | 1589555061 | 0.9961569 | 0.9902191 | 1.0000000 | 0.9859813 | 1.0000000 | 0.9719626 | 0.9444444 | 1.0000000 | 0.8888889 | 0.9714286 | 1.0000000 | 0.9428571 | 1589555244 | 0.9905232 | 0.9794706 | 1.0000000 | 0.9579439 | 0.9345794 | 0.9813084 | 0.9166667 | 0.9444444 | 0.8888889 | 0.9571429 | 0.9714286 | 0.9428571 |
| 6 | sigtopHolm | No | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.139.5p + hsa.miR.199a.5p + hsa.miR.338.3p + hsa.miR.199b.5p | 1589555069 | 0.9961569 | 0.9902191 | 1.0000000 | 0.9859813 | 1.0000000 | 0.9719626 | 0.9444444 | 1.0000000 | 0.8888889 | 0.9714286 | 1.0000000 | 0.9428571 | 1589555252 | 0.9905232 | 0.9794706 | 1.0000000 | 0.9579439 | 0.9345794 | 0.9813084 | 0.9166667 | 0.9444444 | 0.8888889 | 0.9571429 | 0.9714286 | 0.9428571 |
| 7 | topFC | No | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p | 1589555076 | 0.9939733 | 0.9856621 | 1.0000000 | 0.9813084 | 0.9906542 | 0.9719626 | 0.9444444 | 1.0000000 | 0.8888889 | 0.9857143 | 1.0000000 | 0.9714286 | 1589555260 | 0.9944537 | 0.9893380 | 0.9995693 | 0.9579439 | 0.9906542 | 0.9252336 | 0.9305556 | 0.9722222 | 0.8888889 | 0.9714286 | 1.0000000 | 0.9428571 |
| 8 | sigtopSMOTE | Yes | Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p | 1589555086 | 0.9959498 | 0.9954525 | 0.9964472 | 0.9788441 | 0.9814019 | 0.9763116 | 0.8888889 | 0.9166667 | 0.8611111 | 0.9714286 | 1.0000000 | 0.9428571 | 1589555269 | 0.9999317 | 0.9998628 | 1.0000000 | 0.9989771 | 1.0000000 | 0.9979643 | 0.9305556 | 0.8888889 | 0.9722222 | 0.9428571 | 0.8857143 | 1.0000000 |
| 9 | sigtopBonfSMOTE | Yes | Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p | 1589555105 | 0.9959498 | 0.9954525 | 0.9964472 | 0.9788441 | 0.9814019 | 0.9763116 | 0.8888889 | 0.9166667 | 0.8611111 | 0.9714286 | 1.0000000 | 0.9428571 | 1589555288 | 0.9999317 | 0.9998628 | 1.0000000 | 0.9989771 | 1.0000000 | 0.9979643 | 0.9305556 | 0.8888889 | 0.9722222 | 0.9428571 | 0.8857143 | 1.0000000 |
| 10 | sigtopHolmSMOTE | Yes | Class ~ hsa.let.7c.5p + hsa.miR.16.5p + hsa.miR.20a.5p + hsa.miR.21.5p + hsa.miR.21.3p + hsa.miR.22.3p + hsa.miR.23a.3p + hsa.miR.26a.5p + hsa.miR.26b.5p + hsa.miR.27a.3p + hsa.miR.29a.3p | 1589555124 | 0.9959498 | 0.9954525 | 0.9964472 | 0.9788441 | 0.9814019 | 0.9763116 | 0.8888889 | 0.9166667 | 0.8611111 | 0.9714286 | 1.0000000 | 0.9428571 | 1589555306 | 0.9999317 | 0.9998628 | 1.0000000 | 0.9989771 | 1.0000000 | 0.9979643 | 0.9305556 | 0.8888889 | 0.9722222 | 0.9428571 | 0.8857143 | 1.0000000 |
| 11 | topFCSMOTE | Yes | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p | 1589555144 | 0.9980369 | 0.9976070 | 0.9984667 | 0.9929325 | 1.0000000 | 0.9859350 | 0.9583333 | 1.0000000 | 0.9166667 | 0.9857143 | 1.0000000 | 0.9714286 | 1589555325 | 0.9998280 | 0.9996831 | 0.9999730 | 0.9992096 | 1.0000000 | 0.9984269 | 0.9583333 | 0.9166667 | 1.0000000 | 0.9142857 | 0.8285714 | 1.0000000 |
| 12 | cfsSMOTE | Yes | Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p | 1589555162 | 0.9978472 | 0.9972844 | 0.9984099 | 0.9845167 | 0.9801869 | 0.9888036 | 0.9305556 | 0.9722222 | 0.8888889 | 0.9857143 | 1.0000000 | 0.9714286 | 1589555343 | 0.9997226 | 0.9996019 | 0.9998434 | 0.9986051 | 1.0000000 | 0.9972240 | 0.9444444 | 0.9444444 | 0.9444444 | 0.9571429 | 0.9428571 | 0.9714286 |
| 13 | cfsSMOTE_sig | Yes | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p | 1589555179 | 0.9978472 | 0.9972844 | 0.9984099 | 0.9845167 | 0.9801869 | 0.9888036 | 0.9305556 | 0.9722222 | 0.8888889 | 0.9857143 | 1.0000000 | 0.9714286 | 1589555360 | 0.9997226 | 0.9996019 | 0.9998434 | 0.9986051 | 1.0000000 | 0.9972240 | 0.9444444 | 0.9444444 | 0.9444444 | 0.9571429 | 0.9428571 | 0.9714286 |
Description of columns:
method- accronym for methodSMOTE- if balancing using SMOTE or ROSE was used in training dataset.miRy- formula used (miRNAs selected).*_modelname- the name of.RDSfile placed inmodels/directory, containing thecaretfinal model that can be used for prediction of new cases. This allows reproducibility of the results. For exampleglm_prefix is set according to the method,glm= logistic regression.*_train_ROCAUC- area under the ROC curve (AUC ROC) on training dataset, indicating general potential of the model.*_train_ROCAUC_lower95CI- lower boundery of 95% confidence interval for AUC ROC.*_train_ROCAUC_upper95CI- upper boundery of 95% confidence interval for AUC ROC.*_train_Accuracy- accuracy on training set.*_train_Sensitivity- sensitivity on training set.*_train_Specificity- sensitivity on training set.
By this logic every parameter is also calculated from testing (_test_) and validation (_valid_) set. If the method generated a probability, a default cutoff is used for all of the predictions.
Let’s see the general performance (accuracy) of methods in the benchmark:
metody = ks.get_benchmark_methods("benchmark.csv") # gets the methods used in benchmark
par(mfrow = c(2, 2))
for (i in 1:length(metody)) {
temp = ks.get_benchmark("benchmark.csv") # loads benchmark
temp2 = dplyr::select(temp, starts_with(paste0(metody[i], "_")))
boxplot(temp[, paste0(metody[i], "_train_Accuracy")], temp[, paste0(metody[i], "_test_Accuracy")], temp[, paste0(metody[i], "_valid_Accuracy")], main = paste0("Method: ",
metody[i]), names = c("Training", "Testing", "Validation"), ylab = "Accuracy", ylim = c(0.5, 1))
tempids = c(match(paste0(metody[i], "_train_Accuracy"), colnames(temp)), match(paste0(metody[i], "_test_Accuracy"), colnames(temp)), match(paste0(metody[i],
"_valid_Accuracy"), colnames(temp)))
}
par(mfrow = c(1, 1))
With miRNAselector package, the final optimal feature signature can be selected in 3 ways:
1. Picking the signture which achived the best accuracy in training, testing and validation: (metaindex = mean of all 3 accuracy metrics)
acc1 = ks.best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = F) # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ] # get top 3 methods
ks.table(best_signatures[, c("metaindex", "method", "miRy")])| metaindex | method | miRy |
|---|---|---|
| 0.9681348 | topFCSMOTE | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.144.5p + hsa.miR.30c.2.3p + hsa.miR.210.3p + hsa.miR.200a.3p |
| 0.9668298 | cfsSMOTE | Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p |
| 0.9668298 | cfsSMOTE_sig | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p |
2. Picking the signture which achived the best accuracy in testing and validation: (metaindex = mean of 2 accuracy metrics)
acc1 = ks.best_signiture_proposals(benchmark_csv = "benchmark.csv", without_train = T) # generates the benchmark sorted by metaindex
best_signatures = acc1[1:3, ] # get top 3 methods
ks.table(best_signatures[, c("metaindex", "method", "miRy")])| metaindex | method | miRy |
|---|---|---|
| 0.9580357 | topFC | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p |
| 0.9544643 | cfsSMOTE | Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p |
| 0.9544643 | cfsSMOTE_sig | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.375.3p + hsa.miR.708.3p |
3. The signture which achived the best sensitivity and specificity in validation: (metaindex = mean of sensivitiy and specificity in validation dataset)
acc = ks.best_signiture_proposals_meta11(benchmark_csv = "benchmark.csv") # generates the benchmark sorted by metaindex
best_signatures = acc[1:3, ] # get top 3 methods
ks.table(best_signatures[, c("metaindex", "method", "miRy")])| metaindex | method | miRy |
|---|---|---|
| 0.9571429 | cfs_sig | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p |
| 0.9571429 | topFC | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p |
| 0.9428571 | cfsSMOTE | Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p |
It is a good practice to assess learning performance for considered signatures across different classification methods. Here, we visualize the over/underfitting of selected methods by comparing accuracy score between testing and validation sets for 3 top scoring signatures across selection of model architectures.
for (i in 1:length(metody)) {
suppressMessages(library(PairedData))
suppressMessages(library(profileR))
pd = paired(as.numeric(acc[1:3, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:3, paste0(metody[i], "_test_Accuracy")]))
colnames(pd) = c("Train Accuracy", "Test Accuracy")
plot2 = ks.profileplot(pd, Method.id = acc$method[1:3], standardize = F)
pd = paired(as.numeric(acc[1:3, paste0(metody[i], "_train_Accuracy")]), as.numeric(acc[1:3, paste0(metody[i], "_valid_Accuracy")]))
colnames(pd) = c("Train Accuracy", "Valid Accuracy")
plot3 = ks.profileplot(pd, Method.id = acc$method[1:3], standardize = F)
pd = paired(as.numeric(acc[1:3, paste0(metody[i], "_test_Accuracy")]), as.numeric(acc[1:3, paste0(metody[i], "_valid_Accuracy")]))
colnames(pd) = c("Test Accuracy", "Valid Accuracy")
plot4 = ks.profileplot(pd, Method.id = acc$method[1:3], standardize = F)
require(gridExtra)
grid.arrange(arrangeGrob(plot2, plot3, ncol = 2, nrow = 1, top = metody[i]))
grid.arrange(arrangeGrob(plot4, ncol = 1, nrow = 1, top = metody[i]))
}
The relationship betweend accuracy on testing and validation sets can also be pictured as scatterplot:
acc2 = acc[1:6, ] # get top 6 methods
accmelt = melt(acc2, id.vars = "method") %>% filter(variable != "metaindex") %>% filter(variable != "miRy")
accmelt = cbind(accmelt, strsplit2(accmelt$variable, "_"))
acctest = accmelt$value[accmelt$`2` == "test"]
accvalid = accmelt$value[accmelt$`2` == "valid"]
accmeth = accmelt$method[accmelt$`2` == "test"]
unique(accmeth)
#> [1] "cfs_sig" "topFC" "cfsSMOTE" "cfsSMOTE_sig" "sigtop"
#> [6] "sigtopBonf"
plot5 = ggplot(, aes(x = as.numeric(acctest), y = as.numeric(accvalid), shape = accmeth)) + geom_point() + scale_x_continuous(name = "Accuracy on test set",
limits = c(0.5, 1)) + scale_y_continuous(name = "Accuracy on validation set", limits = c(0.5, 1)) + theme_bw()
grid.arrange(arrangeGrob(plot5, ncol = 1, nrow = 1))
7 Best signture analysis
Suppose we decide to use sensitivity and specificity in validation set (e.g. in the model architectures we plan to use in our research) as decisive scoring metric for feature signature. The three best signatures may be:
ks.table(best_signatures[1:3, 2:4])| method | SMOTE | miRy |
|---|---|---|
| cfs_sig | No | Class ~ hsa.miR.21.5p + hsa.miR.30e.3p + hsa.miR.30a.3p + hsa.miR.30c.2.3p + hsa.miR.132.3p + hsa.miR.375.3p + hsa.miR.217.5p + hsa.miR.338.3p + hsa.miR.199b.5p + hsa.miR.381.3p + hsa.miR.199a.3p + hsa.miR.194.5p + hsa.miR.134.5p + hsa.miR.192.5p + hsa.miR.200a.3p + hsa.miR.181c.3p + hsa.miR.29a.3p + hsa.miR.378a.3p + hsa.miR.144.5p + hsa.miR.335.3p + hsa.miR.126.5p + hsa.let.7c.5p + hsa.miR.378a.5p + hsa.miR.181c.5p + hsa.miR.126.3p + hsa.miR.185.5p + hsa.miR.29c.3p + hsa.miR.151a.5p + hsa.miR.92b.3p + hsa.miR.10b.5p + hsa.miR.195.5p + hsa.miR.101.3p + hsa.miR.484 + hsa.miR.28.3p |
| topFC | No | Class ~ hsa.miR.217.5p + hsa.miR.375.3p + hsa.miR.192.5p + hsa.miR.194.5p + hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.199b.5p + hsa.miR.200a.3p + hsa.miR.708.3p + hsa.miR.144.5p + hsa.miR.141.3p |
| cfsSMOTE | Yes | Class ~ hsa.miR.21.5p + hsa.miR.30a.3p + hsa.miR.30e.3p + hsa.miR.375.3p + hsa.miR.708.3p |
To get the miRNAs from formula you can use ks.get_miRNAs_from_benchmark.
selected_miRNAs = ks.get_miRNAs_from_benchmark(benchmark_csv = "benchmark.csv", best_signatures$method[1]) # for the best performing signiture
gsub("\\.", "-", selected_miRNAs) # R doesn't like hyphens, but we can introduce them easly
#> [1] "hsa-miR-21-5p" "hsa-miR-30e-3p" "hsa-miR-30a-3p" "hsa-miR-30c-2-3p"
#> [5] "hsa-miR-132-3p" "hsa-miR-375-3p" "hsa-miR-217-5p" "hsa-miR-338-3p"
#> [9] "hsa-miR-199b-5p" "hsa-miR-381-3p" "hsa-miR-199a-3p" "hsa-miR-194-5p"
#> [13] "hsa-miR-134-5p" "hsa-miR-192-5p" "hsa-miR-200a-3p" "hsa-miR-181c-3p"
#> [17] "hsa-miR-29a-3p" "hsa-miR-378a-3p" "hsa-miR-144-5p" "hsa-miR-335-3p"
#> [21] "hsa-miR-126-5p" "hsa-let-7c-5p" "hsa-miR-378a-5p" "hsa-miR-181c-5p"
#> [25] "hsa-miR-126-3p" "hsa-miR-185-5p" "hsa-miR-29c-3p" "hsa-miR-151a-5p"
#> [29] "hsa-miR-92b-3p" "hsa-miR-10b-5p" "hsa-miR-195-5p" "hsa-miR-101-3p"
#> [33] "hsa-miR-484" "hsa-miR-28-3p"As a double check, we can inspect the differential expression of miRNAs constituating selected signature:
best_de = ks.best_signiture_de(selected_miRNAs)
ks.table(best_de)| miR | log2FC | p-value BH | |
|---|---|---|---|
| 1 | hsa.miR.21.5p | 2.6022157 | 0.0000000 |
| 2 | hsa.miR.30e.3p | -1.3939819 | 0.0000000 |
| 3 | hsa.miR.30a.3p | -2.4419651 | 0.0000000 |
| 4 | hsa.miR.30c.2.3p | -2.0824306 | 0.0000000 |
| 5 | hsa.miR.132.3p | 1.3642193 | 0.0000000 |
| 6 | hsa.miR.375.3p | 4.7881053 | 0.0000000 |
| 7 | hsa.miR.217.5p | 4.9968529 | 0.0000000 |
| 10 | hsa.miR.338.3p | 1.6447027 | 0.0000000 |
| 11 | hsa.miR.199b.5p | 2.3814574 | 0.0000000 |
| 13 | hsa.miR.381.3p | 1.6878957 | 0.0000000 |
| 15 | hsa.miR.199a.3p | 1.2540293 | 0.0000000 |
| 18 | hsa.miR.194.5p | 2.9439150 | 0.0000000 |
| 19 | hsa.miR.134.5p | 1.3684465 | 0.0000000 |
| 23 | hsa.miR.192.5p | 2.9636965 | 0.0000000 |
| 25 | hsa.miR.200a.3p | 2.1949415 | 0.0000000 |
| 27 | hsa.miR.181c.3p | 0.9386203 | 0.0000000 |
| 33 | hsa.miR.29a.3p | -0.6991346 | 0.0000000 |
| 34 | hsa.miR.378a.3p | -1.1444252 | 0.0000000 |
| 39 | hsa.miR.144.5p | -2.1127868 | 0.0000000 |
| 41 | hsa.miR.335.3p | 1.0571023 | 0.0000000 |
| 42 | hsa.miR.126.5p | -1.1663511 | 0.0000000 |
| 45 | hsa.let.7c.5p | -0.8775535 | 0.0000000 |
| 49 | hsa.miR.378a.5p | -1.0287466 | 0.0000000 |
| 57 | hsa.miR.181c.5p | 0.8614935 | 0.0000002 |
| 58 | hsa.miR.126.3p | -0.9851906 | 0.0000005 |
| 61 | hsa.miR.185.5p | 0.6922687 | 0.0000020 |
| 62 | hsa.miR.29c.3p | -0.7856959 | 0.0000026 |
| 65 | hsa.miR.151a.5p | 0.5057800 | 0.0000040 |
| 73 | hsa.miR.92b.3p | 0.7783325 | 0.0000088 |
| 77 | hsa.miR.10b.5p | -1.2777969 | 0.0000396 |
| 84 | hsa.miR.195.5p | -0.7802161 | 0.0003412 |
| 90 | hsa.miR.101.3p | -0.5956161 | 0.0015624 |
| 106 | hsa.miR.484 | -0.3113168 | 0.0182773 |
| 113 | hsa.miR.28.3p | -0.2419443 | 0.0355939 |
Let’s visualize the performance of those methods using barplots:
for (i in 1:3) {
cat(paste0("\n\n## ", acc$method[i], "\n\n"))
par(mfrow = c(1, 2))
acc = ks.best_signiture_proposals_meta11("benchmark.csv")
metody = ks.get_benchmark_methods("benchmark.csv")
ktory_set = match(acc$method[i], ks.get_benchmark("benchmark.csv")$method)
# do_ktorej_kolumny = which(colnames(acc) == 'metaindex') barplot(as.numeric(acc[i,1:do_ktorej_kolumny]))
for (ii in 1:length(metody)) {
temp = ks.get_benchmark("benchmark.csv") %>% dplyr::select(starts_with(paste0(metody[ii], "_t")), starts_with(paste0(metody[ii], "_v")))
ROCtext = paste0("Training AUC ROC: ", round(temp[ktory_set, 1], 2), " (95%CI: ", round(temp[ktory_set, 2], 2), "-", round(temp[ktory_set, 3],
2), ")")
temp = temp[, -c(1:3)]
temp2 = as.numeric(temp[ktory_set, ])
temp3 = matrix(temp2, nrow = 3, byrow = T)
colnames(temp3) = c("Accuracy", "Sensitivity", "Specificity")
rownames(temp3) = c("Training", "Testing", "Validation")
temp3 = t(temp3)
plot1 = barplot(temp3, beside = T, ylim = c(0, 1), xlab = paste0(ROCtext, "\nBlack - accuracy, blue - sensitivity, green - specificity"), width = 0.85,
col = c("black", "blue", "green"), legend = F, args.legend = list(x = "topright", bty = "n", inset = c(0, -0.25)), cex.lab = 0.7, main = paste0(acc$method[i],
" - ", metody[ii]), font.lab = 2)
## Add text at top of bars
text(x = plot1, y = as.numeric(temp3), label = paste0(round(as.numeric(temp[ktory_set, ]) * 100, 1), "%"), pos = 3, cex = 0.6, col = "red")
}
par(mfrow = c(1, 1))
}
#>
#>
#> ## cfs_sig
#>
#>
#> ## topFC
#>
#>
#> ## cfsSMOTE
Finally, we can assess the overlap of top 3 feature selection methods:
overlap = ks.miRNA_signiture_overlap(acc$method[1:3], "benchmark.csv")
Which miRNAs are common for between feature selection methods?
attr(overlap, "intersections")
#> $`cfs_sig:topFC`
#> [1] "hsa.miR.217.5p" "hsa.miR.199b.5p" "hsa.miR.194.5p" "hsa.miR.192.5p"
#> [5] "hsa.miR.200a.3p" "hsa.miR.144.5p"
#>
#> $`topFC:cfsSMOTE`
#> [1] "hsa.miR.708.3p"
#>
#> $`cfs_sig:cfsSMOTE`
#> [1] "hsa.miR.30e.3p"
#>
#> $`cfs_sig:topFC:cfsSMOTE`
#> [1] "hsa.miR.21.5p" "hsa.miR.30a.3p" "hsa.miR.375.3p"
#>
#> $topFC
#> [1] "hsa.miR.141.3p"
#>
#> $cfs_sig
#> [1] "hsa.miR.30c.2.3p" "hsa.miR.132.3p" "hsa.miR.338.3p" "hsa.miR.381.3p"
#> [5] "hsa.miR.199a.3p" "hsa.miR.134.5p" "hsa.miR.181c.3p" "hsa.miR.29a.3p"
#> [9] "hsa.miR.378a.3p" "hsa.miR.335.3p" "hsa.miR.126.5p" "hsa.let.7c.5p"
#> [13] "hsa.miR.378a.5p" "hsa.miR.181c.5p" "hsa.miR.126.3p" "hsa.miR.185.5p"
#> [17] "hsa.miR.29c.3p" "hsa.miR.151a.5p" "hsa.miR.92b.3p" "hsa.miR.10b.5p"
#> [21] "hsa.miR.195.5p" "hsa.miR.101.3p" "hsa.miR.484" "hsa.miR.28.3p"Let’s draw vulcano plot and mark the miRNAs selected in best signature:
ks.vulcano_plot(selected_miRNAs = de$miR, DE = de, only_label = selected_miRNAs)
Let’s draw heatmap for selected miRNAs in whole dataset (training, testing and validation set).
ks.heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = F, margins = c(10,
10))
ks.heatmap(x = dplyr::select(mixed, gsub("\\.", "-", selected_miRNAs)), rlab = data.frame(Class = mixed$Class, Mix = mixed$mix), zscore = T, margins = c(10,
10))
Based on everything we have done so far, we suggest using the following signiture in further validation of biomarker study.
cat(paste0(gsub("\\.", "-", selected_miRNAs), collapse = ", "))
#> hsa-miR-21-5p, hsa-miR-30e-3p, hsa-miR-30a-3p, hsa-miR-30c-2-3p, hsa-miR-132-3p, hsa-miR-375-3p, hsa-miR-217-5p, hsa-miR-338-3p, hsa-miR-199b-5p, hsa-miR-381-3p, hsa-miR-199a-3p, hsa-miR-194-5p, hsa-miR-134-5p, hsa-miR-192-5p, hsa-miR-200a-3p, hsa-miR-181c-3p, hsa-miR-29a-3p, hsa-miR-378a-3p, hsa-miR-144-5p, hsa-miR-335-3p, hsa-miR-126-5p, hsa-let-7c-5p, hsa-miR-378a-5p, hsa-miR-181c-5p, hsa-miR-126-3p, hsa-miR-185-5p, hsa-miR-29c-3p, hsa-miR-151a-5p, hsa-miR-92b-3p, hsa-miR-10b-5p, hsa-miR-195-5p, hsa-miR-101-3p, hsa-miR-484, hsa-miR-28-3p8 Sesssion
session_info()
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#> setting value
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#> collate C
#> ctype en_US.UTF-8
#> tz Europe/Warsaw
#> date 2020-05-15
#>
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#> [4] /usr/lib/R/library
#>
#> P ── Loaded and on-disk path mismatch.packageDescription("miRNAselector")
#> Package: miRNAselector
#> Type: Package
#> Title: miRNAselect - a package for biomarker miRNA selection based on
#> miRNA-seq NGS data.
#> Version: 0.1.0
#> Author: Konrad Stawiski
#> Maintainer: Konrad Stawiski <konrad@konsta.com.pl>
#> Description: To be completed... A package for biomarker miRNA selection
#> based on miRNA-seq NGS data.
#> License: License: MIT + file LICENSE
#> Encoding: UTF-8
#> LazyData: true
#> Suggests: knitr, rmarkdown,
#> VignetteBuilder: knitr
#> StagedInstall: no
#> Imports: dplyr, remotes, devtools, BiocManager, plyr, epiDisplay, rsq,
#> MASS, caret, pROC, ggplot2, DMwR, ROSE, gridExtra, gplots,
#> stringr, data.table, doParallel, Boruta, spFSR, varSelRF,
#> My.stepwise, psych, C50, randomForest, nnet, reticulate,
#> stargazer, ggrepel, classInt, plotly, keras, cutpointr, naniar,
#> visdat, imputeMissings, foreach, deepnet, snow, calibrate,
#> networkD3, VennDiagram, RSNNS, kernlab, car, PairedData,
#> profileR, xgboost, kableExtra, doSNOW, curl, rJava, mice,
#> MatchIt, cluster
#> RoxygenNote: 7.1.0
#>
#> -- File: /home/konrad/snorlax/miRNAselector/DESCRIPTIONTo render this tutorial we used:
render("Tutorial.Rmd", output_file = "Tutorial.html", output_dir = "../static/")Packages installed in our docker enviorment:
ks.table(as.data.frame(installed.packages()))| Package | LibPath | Version | Priority | Depends | Imports | LinkingTo | Suggests | Enhances | License | License_is_FOSS | License_restricts_use | OS_type | MD5sum | NeedsCompilation | Built | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ALL | ALL | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.26.0 | NA | R (>= 2.10), Biobase (>= 2.5.5) | NA | NA | rpart | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| AnnotationDbi | AnnotationDbi | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.46.1 | NA | R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges | DBI, RSQLite, S4Vectors (>= 0.9.25) | NA | hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| BBmisc | BBmisc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.11 | NA | NA | utils, methods, stats, checkmate (>= 1.8.0) | NA | testthat, microbenchmark, codetools | NA | BSD_2_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| BGLR | BGLR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.8 | NA | R (>= 3.5.0) | truncnorm | NA | NA | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| BH | BH | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.72.0-3 | NA | NA | NA | NA | NA | NA | BSL-1.0 | NA | NA | NA | NA | no | 3.6.1 |
| Biobase | Biobase | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.44.0 | NA | R (>= 2.10), BiocGenerics (>= 0.27.1), utils | methods | NA | tools, tkWidgets, ALL, RUnit, golubEsets | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |
| BiocCheck | BiocCheck | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.20.0 | NA | R (>= 3.5.0) | biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr, tools, optparse, codetools, methods, utils, knitr | NA | RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools (>= 1.4.1), usethis, BiocStyle | codetoolsBioC | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.2 |
| BiocGenerics | BiocGenerics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.30.0 | NA | R (>= 3.6.0), methods, utils, graphics, stats, parallel | methods, utils, graphics, stats, parallel | NA | Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |
| BiocManager | BiocManager | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.30.10 | NA | NA | utils | NA | BiocStyle, BiocVersion, remotes, testthat, withr, curl, knitr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| BiocNeighbors | BiocNeighbors | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.0 | NA | NA | Rcpp, BiocGenerics, S4Vectors, BiocParallel, stats, methods | Rcpp, RcppAnnoy, RcppHNSW | testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| BiocParallel | BiocParallel | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.18.1 | NA | methods | stats, utils, futile.logger, parallel, snow | BH | BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| BiocSingular | BiocSingular | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | NA | BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, irlba, rsvd, Rcpp | Rcpp, beachmat | testthat, BiocStyle, knitr, rmarkdown, beachmat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| BiocStyle | BiocStyle | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.12.0 | NA | NA | bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager | NA | BiocGenerics, RUnit, htmltools | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.2 |
| BiocVersion | BiocVersion | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.9.0 | NA | R (>= 3.6.0), R (< 3.7.0) | NA | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |
| Biocomb | Biocomb | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4 | NA | R (>= 2.13.0),gtools,Rcpp (>= 0.12.1) | rgl, MASS, e1071, randomForest, pROC, ROCR, arules, pamr, class, nnet, rpart, FSelector, RWeka, grDevices, graphics, stats, utils | Rcpp | NA | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.2 |
| Biostrings | Biostrings | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.52.0 | NA | R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13), IRanges, XVector (>= 0.23.2) | graphics, methods, stats, utils | S4Vectors, IRanges, XVector | BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit | Rmpi | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| Boruta | Boruta | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 6.0.0 | NA | ranger | NA | NA | mlbench, rFerns, randomForest, testthat, xgboost | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| BradleyTerry2 | BradleyTerry2 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-2 | NA | R (>= 2.10) | brglm, gtools, lme4 (>= 1.0), qvcalc, stats | NA | prefmod, testthat | gnm | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| C50 | C50 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.3 | NA | R (>= 2.10.0) | partykit, Cubist (>= 0.2.3) | NA | knitr, modeldata | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| CGEN | CGEN | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.20.0 | NA | R (>= 2.10.1), survival, mvtnorm | NA | NA | cluster | NA | GPL-2 + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| Cairo | Cairo | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5-12 | NA | R (>= 2.4.0) | grDevices, graphics | NA | png | FastRWeb | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| CircStats | CircStats | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2-6 | NA | MASS, boot | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| ComplexHeatmap | ComplexHeatmap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.0 | NA | R (>= 3.1.2), methods, grid, graphics, stats, grDevices | circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png | NA | testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| ConsensusClusterPlus | ConsensusClusterPlus | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.48.0 | NA | NA | Biobase, ALL, graphics, stats, utils, cluster | NA | NA | NA | GPL version 2 | NA | NA | NA | NA | no | 3.6.1 |
| Cubist | Cubist | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.3 | NA | lattice | reshape2, utils | NA | mlbench, caret, knitr, modeldata, dplyr (>= 0.7.4), rlang, tidyrules | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| DBI | DBI | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | methods, R (>= 3.0.0) | NA | NA | blob, covr, hms, knitr, magrittr, rmarkdown, rprojroot, RSQLite (>= 1.1-2), testthat, xml2 | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.1 |
| DESeq | DESeq | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.36.0 | NA | BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice | genefilter, geneplotter, methods, MASS, RColorBrewer | NA | pasilla (>= 0.2.10), vsn, gplots | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.1 |
| DESeq2 | DESeq2 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.24.0 | NA | S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) | BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0) | Rcpp, RcppArmadillo | testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10) | NA | LGPL (>= 3) | NA | NA | NA | NA | yes | 3.6.0 |
| DEoptimR | DEoptimR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-8 | NA | NA | stats | NA | NA | robustbase | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| DMwR | DMwR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.1 | NA | R(>= 2.10), methods, graphics, lattice (>= 0.18-3), grid (>= 2.10.1) | xts (>= 0.6-7), quantmod (>= 0.3-8), zoo (>= 1.6-4), abind (>= 1.1-0), rpart (>= 3.1-46), class (>= 7.3-1), ROCR (>= 1.0) | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| DO.db | DO.db | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.9 | NA | R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7) | methods, AnnotationDbi | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| DOSE | DOSE | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.10.2 | NA | R (>= 3.4.0) | AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim (>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils | NA | prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| DT | DT | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.13 | NA | NA | htmltools (>= 0.3.6), htmlwidgets (>= 1.3), jsonlite (>= 0.9.16), magrittr, crosstalk, promises | NA | knitr (>= 1.8), rmarkdown, shiny (>= 1.2.0) | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| DelayedArray | DelayedArray | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.10.0 | NA | R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.27.1), S4Vectors (>= 0.21.7), IRanges (>= 2.17.3), BiocParallel | stats, Matrix | S4Vectors | Matrix, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |
| DelayedMatrixStats | DelayedMatrixStats | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.1 | NA | DelayedArray (>= 0.9.8) | methods, matrixStats (>= 0.55.0), Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.7.10), BiocParallel | NA | testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| DendSer | DendSer | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | gclus,seriation | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| Deriv | Deriv | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.0 | NA | NA | methods | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| DiagrammeR | DiagrammeR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.6.1 | NA | R (>= 3.2.0) | dplyr (>= 0.7.6), downloader (>= 0.4), glue (>= 1.3.0), htmltools (>= 0.3.6), htmlwidgets (>= 1.2), igraph (>= 1.2.2), influenceR (>= 0.1.0), magrittr (>= 1.5), purrr (>= 0.2.5), RColorBrewer (>= 1.1-2), readr (>= 1.1.1), rlang (>= 0.2.2), rstudioapi (>= 0.7), scales (>= 1.0.0), stringr (>= 1.3.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), viridis (>= 0.5.1), visNetwork (>= 2.0.4) | NA | covr, DiagrammeRsvg, rsvg, knitr, testthat, rmarkdown | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| DynNom | DynNom | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.0.1 | NA | magrittr | survival (>= 2.38-3), shiny, ggplot2 (> 2.1.0), plotly, stargazer, prediction, rms, dplyr, compare, BBmisc | NA | gam, mgcv | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| EDASeq | EDASeq | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.18.0 | NA | Biobase (>= 2.15.1), ShortRead (>= 1.11.42) | methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq, aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager | NA | BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| EnhancedVolcano | EnhancedVolcano | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.5 | NA | ggplot2, ggrepel | NA | RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, gridExtra, magrittr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 | |
| FNN | FNN | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.3 | NA | R (>= 3.0.0) | NA | NA | chemometrics, mvtnorm | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| FSelector | FSelector | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.31 | NA | NA | randomForest, RWeka, digest, entropy | NA | mlbench, rpart | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| FactoMineR | FactoMineR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3 | NA | R (>= 3.5.0) | car,cluster,ellipse,flashClust,graphics,grDevices,lattice,leaps,MASS,scatterplot3d,stats,utils,ggplot2,ggrepel | NA | missMDA,knitr,Factoshiny | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| Formula | Formula | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2-3 | NA | R (>= 2.0.0), stats | NA | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| GA | GA | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.2.1 | NA | R (>= 3.4), methods, foreach, iterators | stats, graphics, grDevices, utils, cli, crayon, Rcpp | Rcpp, RcppArmadillo | parallel, doParallel, doRNG (>= 1.6), knitr (>= 1.8) | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| GDCRNATools | GDCRNATools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.1 | NA | R (>= 3.5.0) | shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel | NA | knitr, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.2 |
| GGally | GGally | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.0 | NA | R (>= 3.1), ggplot2 (> 2.2.0) | grDevices, grid, gtable (>= 0.2.0), plyr (>= 1.8.3), progress, RColorBrewer, reshape (>= 0.8.5), utils, rlang | NA | broom (>= 0.4.0), chemometrics, geosphere (>= 1.5-1), igraph (>= 1.0.1), intergraph (>= 2.0-2), maps (>= 3.1.0), mapproj, network (>= 1.12.0), scagnostics, scales (>= 0.4.0), sna (>= 2.3-2), survival, packagedocs (>= 0.4.0), rmarkdown, roxygen2, testthat, crosstalk | NA | GPL (>= 2.0) | NA | NA | NA | NA | no | 3.6.2 |
| GO.db | GO.db | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.8.2 | NA | R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1) | methods, AnnotationDbi | NA | DBI | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| GOSemSim | GOSemSim | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.10.0 | NA | R (>= 3.4.0) | AnnotationDbi, GO.db, methods, utils | Rcpp | AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| GenomeInfoDb | GenomeInfoDb | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.20.0 | NA | R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12) | stats, stats4, utils, RCurl, GenomeInfoDbData | NA | GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |
| GenomeInfoDbData | GenomeInfoDbData | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.1 | NA | R (>= 3.5.0) | NA | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |
| GenomicAlignments | GenomicAlignments | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.20.1 | NA | R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.19.11), IRanges (>= 2.15.12), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.33.4), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2) | methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel | S4Vectors, IRanges | ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| GenomicDataCommons | GenomicDataCommons | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8.0 | NA | R (>= 3.4.0), magrittr | stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble | NA | BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| GenomicFeatures | GenomicFeatures | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.36.4 | NA | BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.15.4), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) | methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) | NA | RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| GenomicRanges | GenomicRanges | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.36.1 | NA | R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.19.11), IRanges (>= 2.17.1), GenomeInfoDb (>= 1.15.2) | utils, stats, XVector (>= 0.19.8) | S4Vectors, IRanges | Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| GetoptLong | GetoptLong | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.8 | NA | R (>= 3.0.0) | rjson, GlobalOptions (>= 0.1.0), methods | NA | testthat (>= 1.0.0), knitr, markdown | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| GlobalOptions | GlobalOptions | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.1 | NA | R (>= 3.3.0), methods | utils | NA | testthat (>= 1.0.0), knitr, markdown | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| HDF5Array | HDF5Array | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.12.3 | NA | R (>= 3.4), methods, DelayedArray (>= 0.9.3), rhdf5 (>= 2.25.6) | utils, tools, BiocGenerics (>= 0.25.1), S4Vectors, IRanges | S4Vectors (>= 0.21.6), Rhdf5lib | h5vcData, SummarizedExperiment (>= 1.9.6), GenomicRanges, ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures, BiocStyle | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| Hmisc | Hmisc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.4-0 | NA | lattice, survival (>= 3.1-6), Formula, ggplot2 (>= 2.2) | methods, latticeExtra, cluster, rpart, nnet, acepack, foreign, gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), viridis, htmltools, base64enc | NA | chron, rms, mice, tables, knitr, ff, ffbase, plotly (>= 4.5.6), rlang | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| IRanges | IRanges | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.18.3 | NA | R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.21.9) | stats4 | S4Vectors | XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| ISwR | ISwR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0-8 | NA | R (>= 2.6.0) | NA | NA | survival,MASS | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| KEGGREST | KEGGREST | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.24.1 | NA | NA | methods, httr, png, Biostrings | NA | RUnit, BiocGenerics, knitr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| KEGGgraph | KEGGgraph | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.44.0 | NA | R (>= 2.10.0) | methods, XML (>= 2.3-0), graph, utils, RCurl | NA | Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| KMsurv | KMsurv | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-5 | NA | NA | NA | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | NA | 3.6.0 |
| LDheatmap | LDheatmap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.99-7 | NA | R (>= 2.14.0) | grid, genetics, snpStats, Rcpp | Rcpp | rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, lattice, ggplot2, vcfR | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| Lahman | Lahman | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 7.0-1 | NA | R (>= 2.10) | dplyr | NA | lattice, ggplot2, googleVis, data.table, vcd, reshape2, tidyr, zipcode, knitr, rmarkdown, car | NA | GPL | NA | NA | NA | NA | no | 3.6.1 |
| LambertW | LambertW | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.4 | NA | MASS, ggplot2, | lamW (>= 1.0.0), stats, graphics, grDevices, RColorBrewer, reshape2, Rcpp | Rcpp, lamW | boot, Rsolnp, nortest, numDeriv, testthat, moments, | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| LiblineaR | LiblineaR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.10-8 | NA | NA | NA | NA | SparseM | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.0 |
| LogicReg | LogicReg | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.2 | NA | R (>= 2.10), survival | stats, graphics, utils, grDevices | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| MASS | MASS | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 7.3-51.6 | recommended | R (>= 3.1.0), grDevices, graphics, stats, utils | methods | NA | lattice, nlme, nnet, survival | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| MLmetrics | MLmetrics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.1 | NA | R (>= 2.10) | stats, utils, ROCR | NA | e1071 | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| MatchIt | MatchIt | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0.2 | NA | R (>= 2.6) | MASS, Matching | NA | cem, nnet, optmatch, rpart, mgcv, WhatIf, R.rsp, testthat, rgenoud | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| Matching | Matching | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.9-7 | NA | R (>= 2.6.0), MASS (>= 7.2-1), graphics, grDevices, stats | NA | NA | parallel, rgenoud (>= 2.12), rbounds | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| MatrixModels | MatrixModels | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-1 | NA | R (>= 3.0.1) | stats, methods, Matrix (>= 1.1-5) | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| ModelMetrics | ModelMetrics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.2.2 | NA | R (>= 3.2.2) | Rcpp, data.table | Rcpp | testthat | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| My.stepwise | My.stepwise | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.0 | NA | R (>= 3.3.3) | car, lmtest, survival, stats | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.2 |
| NLP | NLP | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2-0 | NA | R (>= 3.2.0) | utils | NA | NA | udpipe, spacyr, cleanNLP | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| NOISeq | NOISeq | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.28.0 | NA | R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) | NA | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| PASWR | PASWR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1 | NA | e1071, MASS, lattice | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | NA | 3.6.1 |
| PairedData | PairedData | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.1 | NA | methods,graphics,MASS,gld,mvtnorm,lattice,ggplot2 | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| ParamHelpers | ParamHelpers | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.14 | NA | NA | backports, BBmisc (>= 1.10), checkmate (>= 1.8.2), fastmatch, methods | NA | akima, covr, eaf, emoa, GGally, ggplot2, grid, gridExtra, irace (>= 2.1), lhs, plyr, reshape2, testthat | NA | BSD_2_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| R.methodsS3 | R.methodsS3 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8.0 | NA | R (>= 2.13.0) | utils | NA | codetools | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.2 |
| R.oo | R.oo | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.23.0 | NA | R (>= 2.13.0), R.methodsS3 (>= 1.7.1) | methods, utils | NA | tools | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.1 |
| R.utils | R.utils | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.9.2 | NA | R (>= 2.14.0), R.oo (>= 1.23.0) | methods, utils, tools, R.methodsS3 (>= 1.7.1) | NA | digest (>= 0.6.10) | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.2 |
| R6 | R6 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.4.1 | NA | R (>= 3.0) | NA | NA | knitr, microbenchmark, pryr, testthat, ggplot2, scales | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| RANN | RANN | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.6.1 | NA | NA | NA | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.1 |
| RBGL | RBGL | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.60.0 | NA | graph, methods | methods | BH | Rgraphviz, XML, RUnit, BiocGenerics | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.2 |
| RColorBrewer | RColorBrewer | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-2 | NA | R (>= 2.0.0) | NA | NA | NA | NA | Apache License 2.0 | NA | NA | NA | NA | no | 3.6.0 |
| RCurl | RCurl | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.98-1.2 | NA | R (>= 3.4.0), methods | bitops | NA | XML | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| RISmed | RISmed | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1.7 | NA | R (>= 2.8.0), methods | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| RMySQL | RMySQL | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.10.20 | NA | R (>= 2.8.0), DBI (>= 0.4) | methods | NA | RMariaDB, testthat, curl | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| RNifti | RNifti | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | NA | Rcpp (>= 0.11.0) | Rcpp | testthat (>= 0.11.0), covr, reportr, shades | oro.nifti, tractor.base | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| ROCR | ROCR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-11 | NA | R (>= 3.6) | methods, graphics, grDevices, gplots, stats | NA | testthat, knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| RODBC | RODBC | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-16 | NA | R (>= 3.0.0) | stats | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| ROSE | ROSE | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-3 | NA | NA | NA | NA | MASS, nnet, rpart, tree | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| RPostgreSQL | RPostgreSQL | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6-2 | NA | R (>= 2.9.0), methods, DBI (>= 0.3) | NA | NA | NA | NA | GPL-2 | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| RRF | RRF | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.9.1 | NA | R (>= 2.5.0), stats | NA | NA | RColorBrewer, MASS | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |
| RSNNS | RSNNS | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-12 | NA | R (>= 2.10.0), methods, Rcpp (>= 0.8.5) | NA | Rcpp | scatterplot3d,NeuralNetTools | NA | LGPL (>= 2) | file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| RSQLite | RSQLite | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2.0 | NA | R (>= 3.1.0) | bit64, blob (>= 1.2.0), DBI (>= 1.1.0), memoise, methods, pkgconfig, Rcpp (>= 0.12.7) | BH, plogr (>= 0.2.0), Rcpp | DBItest (>= 1.7.0), knitr, rmarkdown, testthat | NA | LGPL (>= 2.1) | NA | NA | NA | NA | yes | 3.6.1 |
| RSpectra | RSpectra | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.16-0 | NA | R (>= 3.0.2) | Matrix (>= 1.1-0), Rcpp (>= 0.11.5) | Rcpp, RcppEigen (>= 0.3.3.3.0) | knitr, rmarkdown, prettydoc | NA | MPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| RUnit | RUnit | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.32 | NA | R (>= 2.5.0), utils (>= 2.5.0), methods (>= 2.5.0), graphics (>= 2.5.0) | NA | NA | XML (>= 3.1.0) | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| RVAideMemoire | RVAideMemoire | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-75 | NA | NA | ade4 (>= 1.7-8), boot, car, FactoMineR, graphics, grDevices, lme4 (>= 1.0-4), MASS, mixOmics, nnet, pls, pspearman, stats, utils, vegan (>= 2.4-3) | NA | dgof, emmeans, ordinal, survival | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| RViennaCL | RViennaCL | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7.1.8 | NA | NA | NA | NA | gpuR | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| RWeka | RWeka | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-42 | NA | R (>= 2.6.0) | RWekajars (>= 3.9.3-1), rJava (>= 0.6-3), graphics, stats, utils, grid | NA | partykit (>= 0.8.0), mlbench, e1071 | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| RWekajars | RWekajars | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.9.3-2 | NA | NA | rJava (>= 0.6-3) | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| Rcpp | Rcpp | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.4.6 | NA | NA | methods, utils | NA | tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2) | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| RcppAnnoy | RcppAnnoy | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0.16 | NA | R (>= 3.1) | methods, Rcpp (>= 0.11.3) | Rcpp | tinytest | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| RcppArmadillo | RcppArmadillo | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9.870.2.0 | NA | R (>= 3.3.0) | Rcpp (>= 0.11.0), stats, utils, methods | Rcpp | tinytest, Matrix, pkgKitten, reticulate, slam | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| RcppCNPy | RcppCNPy | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.10 | NA | R (>= 3.1.0) | methods, Rcpp | Rcpp | knitr, rmarkdown, pinp, reticulate | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| RcppEigen | RcppEigen | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.3.7.0 | NA | R (>= 2.15.1) | Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils | Rcpp | inline, tinytest, pkgKitten, microbenchmark | NA | GPL (>= 2) | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| RcppHNSW | RcppHNSW | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.0 | NA | NA | methods, Rcpp (>= 0.11.3) | Rcpp | testthat, covr | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| RcppNumerical | RcppNumerical | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-0 | NA | NA | Rcpp | Rcpp, RcppEigen | knitr, rmarkdown, prettydoc, mvtnorm, RcppEigen | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| RcppParallel | RcppParallel | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.0.1 | NA | R (>= 3.0.2) | NA | NA | Rcpp, RUnit, knitr, rmarkdown | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| RcppRoll | RcppRoll | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 2.15.1) | Rcpp | Rcpp | zoo, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |
| RefManageR | RefManageR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.12 | NA | R (>= 3.0) | xml2, jsonlite, utils, plyr, tools, httr, bibtex (>= 0.4.1), lubridate (>= 1.5.0), stringr, methods | NA | knitr, testthat, | NA | GPL-2 | GPL-3 | BSD_3_clause + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| Rgraphviz | Rgraphviz | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.28.0 | NA | R (>= 2.6.0), methods, utils, graph, grid | stats4, graphics, grDevices | NA | RUnit, BiocGenerics, XML | NA | EPL | NA | NA | NA | NA | yes | 3.6.1 |
| Rhdf5lib | Rhdf5lib | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.3 | NA | NA | NA | NA | BiocStyle, knitr, rmarkdown | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| Rhtslib | Rhtslib | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.16.3 | NA | NA | zlibbioc | zlibbioc | BiocStyle, knitr | NA | LGPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| Rook | Rook | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-1 | NA | R (>= 2.13.0) | utils, tools, methods, brew | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| Rsamtools | Rsamtools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.3 | NA | methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6) | utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel | Rhtslib (>= 1.16.3), S4Vectors, IRanges, XVector, Biostrings | GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle | NA | Artistic-2.0 | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| Rsubread | Rsubread | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.34.7 | NA | NA | grDevices, stats, utils | NA | NA | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| S4Vectors | S4Vectors | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.22.1 | NA | R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>= 0.23.3) | NA | NA | IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| SQUAREM | SQUAREM | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2020.2 | NA | R (>= 3.0) | NA | NA | setRNG | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| ShortRead | ShortRead | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.42.0 | NA | BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) | Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, | S4Vectors, IRanges, XVector, Biostrings | BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| SingleCellExperiment | SingleCellExperiment | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.0 | NA | SummarizedExperiment | S4Vectors, methods, BiocGenerics, utils, stats | NA | testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne, Matrix | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| SnowballC | SnowballC | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7.0 | NA | NA | NA | NA | NA | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| SparseM | SparseM | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.78 | NA | R (>= 2.15), methods | graphics, stats, utils | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| SpidermiR | SpidermiR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.14.0 | NA | R (>= 3.0.0) | networkD3, httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots, grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks, gdata | NA | BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| SummarizedExperiment | SummarizedExperiment | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.14.1 | NA | R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase, DelayedArray (>= 0.3.20) | utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.17.25), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.13.1) | NA | annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| SuppDists | SuppDists | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-9.5 | NA | R (>= 3.3.0) | NA | NA | RcppZiggurat | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| Sushi | Sushi | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.22.0 | NA | R (>= 2.10), zoo,biomaRt | graphics, grDevices | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| TCGAbiolinks | TCGAbiolinks | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.12.6 | NA | R (>= 3.5) | downloader (>= 0.4), survminer, grDevices, dplyr, gridExtra, graphics, tibble, grid, GenomicRanges, XML (>= 3.98.0), data.table, EDASeq (>= 2.0.0), edgeR (>= 3.0.0), jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, ggthemes, survival, stringr (>= 1.0.0), IRanges, scales, rvest (>= 0.3.0), stats, utils, selectr, S4Vectors, ComplexHeatmap (>= 1.10.2), R.utils, SummarizedExperiment (>= 1.4.0), genefilter, ConsensusClusterPlus, readr, RColorBrewer, doParallel, GenomeInfoDb, GenomicFeatures, parallel, tools, tidyr, sva, limma, purrr, xml2, httr (>= 1.2.1), matlab, circlize, ggrepel (>= 0.6.3) | NA | jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, igraph, supraHex | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| TH.data | TH.data | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-10 | NA | R (>= 2.10.0), survival, MASS | NA | NA | dplyr, gdata, plyr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| TSP | TSP | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-10 | NA | R (>= 3.5.0) | graphics, foreach, utils, stats, grDevices | NA | sp, maps, maptools, testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| TTR | TTR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.23-6 | NA | NA | xts (>= 0.10-0), zoo, curl | xts | RUnit | quantmod | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| TeachingDemos | TeachingDemos | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.12 | NA | R (>= 2.10) | NA | NA | tkrplot, lattice, MASS, rgl, tcltk, tcltk2, png, ggplot2, logspline, maptools, R2wd, manipulate | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.2 |
| UpSetR | UpSetR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.0 | NA | R (>= 3.0) | ggplot2, gridExtra, plyr, utils, stats, methods, grDevices, scales | NA | knitr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| VIM | VIM | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 6.0.0 | NA | R (>= 3.5.0),colorspace,grid | car, grDevices, magrittr, robustbase, stats, sp, vcd,MASS,nnet,e1071,methods,Rcpp,utils,graphics,laeken,ranger, data.table(>= 1.9.4) | Rcpp | dplyr, testthat (>= 2.1.0), knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| VennDiagram | VennDiagram | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.20 | NA | R (>= 2.14.1), grid (>= 2.14.1), futile.logger | NA | NA | testthat | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| XLConnect | XLConnect | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | R (>= 2.10.0) | methods, rJava | NA | RUnit, lattice, ggplot2 (>= 0.9.3), zoo | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| XLConnectJars | XLConnectJars | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2-15 | NA | NA | rJava | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| XML | XML | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.99-0.3 | NA | R (>= 2.13.0), methods, utils | NA | NA | bitops, RCurl | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| XVector | XVector | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.24.0 | NA | R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= 0.21.13), IRanges (>= 2.15.12) | methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges | S4Vectors, IRanges | Biostrings, drosophila2probe, RUnit | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |
| abind | abind | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-5 | NA | R (>= 1.5.0) | methods, utils | NA | NA | NA | LGPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| acepack | acepack | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.1 | NA | NA | NA | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| ada | ada | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0-5 | NA | R(>= 2.10),rpart | NA | NA | NA | NA | GPL | NA | NA | NA | NA | no | 3.6.1 |
| additivityTests | additivityTests | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-4 | NA | NA | NA | NA | knitr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| ade4 | ade4 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7-15 | NA | R (>= 2.10) | graphics, grDevices, methods, stats, utils, MASS, pixmap, sp | NA | ade4TkGUI, adegraphics, adephylo, ape, CircStats, deldir, lattice, spdep, splancs, waveslim | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| affy | affy | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.62.0 | NA | R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) | affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc | preprocessCore | tkWidgets (>= 1.19.0), affydata, widgetTools | NA | LGPL (>= 2.0) | NA | NA | NA | NA | yes | 3.6.1 |
| affyio | affyio | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.54.0 | NA | R (>= 2.6.0) | zlibbioc, methods | NA | NA | NA | LGPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| amap | amap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.8-18 | NA | R (>= 3.6.0) | NA | NA | Biobase | NA | GPL | NA | NA | NA | NA | yes | 3.6.1 |
| annotate | annotate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.62.0 | NA | R (>= 2.10), AnnotationDbi (>= 1.27.5), XML | Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), RCurl | NA | hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |
| ape | ape | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.3 | NA | R (>= 3.2.0) | nlme, lattice, graphics, methods, stats, tools, utils, parallel, Rcpp (>= 0.12.0) | Rcpp | gee, expm, igraph | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| apeglm | apeglm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.0 | NA | NA | emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp | Rcpp, RcppEigen, RcppNumerical | DESeq2, airway, knitr, rmarkdown, testthat | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| aroma.light | aroma.light | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.14.0 | NA | R (>= 2.15.2) | stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.22.0), R.utils (>= 2.7.0), matrixStats (>= 0.54.0) | NA | princurve (>= 2.1.2) | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| arules | arules | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6-5 | NA | R (>= 3.4.0), Matrix (>= 1.2-0) | stats, methods, graphics, utils | NA | pmml, XML, arulesViz, testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| arulesViz | arulesViz | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-3 | NA | arules (>= 1.4.1), grid | scatterplot3d, vcd, seriation, igraph (>= 1.0.0), graphics, methods, utils, grDevices, stats, colorspace, DT, plotly, visNetwork | NA | graph, Rgraphviz, iplots, shiny, shinythemes, htmlwidgets | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| askpass | askpass | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1 | NA | NA | sys (>= 2.1) | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| assertive | assertive | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3-5 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-4), assertive.properties (>= 0.0-2), assertive.types (>= 0.0-2), assertive.numbers, assertive.strings, assertive.datetimes, assertive.files, assertive.sets (>= 0.0-2), assertive.matrices, assertive.models, assertive.data, assertive.data.uk, assertive.data.us, assertive.reflection (>= 0.0-2), assertive.code, knitr | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.base | assertive.base | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-7 | NA | R (>= 3.0.0) | methods, utils | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.code | assertive.code | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-3 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), assertive.properties, assertive.types, methods | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.data | assertive.data | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-3 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), assertive.strings | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.data.uk | assertive.data.uk | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), assertive.strings | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.data.us | assertive.data.us | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), assertive.strings | NA | testthat, devtools | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.datetimes | assertive.datetimes | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), assertive.types | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.files | assertive.files | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), assertive.numbers | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.matrices | assertive.matrices | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2) | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.models | assertive.models | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), stats | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.numbers | assertive.numbers | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2) | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.properties | assertive.properties | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-4 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-7), methods | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.reflection | assertive.reflection | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-4 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-7), utils | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.sets | assertive.sets | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-3 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-7) | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.strings | assertive.strings | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-3 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-2), assertive.types, stringi | NA | testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertive.types | assertive.types | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-3 | NA | R (>= 3.0.0) | assertive.base (>= 0.0-7), assertive.properties, codetools, methods, stats | NA | testthat, data.table, dplyr, xml2 | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| assertthat | assertthat | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.1 | NA | NA | tools | NA | testthat, covr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| backports | backports | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.7 | NA | R (>= 3.0.0) | utils | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| bartMachine | bartMachine | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.4.2 | NA | R (>= 2.14.0), rJava (>= 0.9-8), bartMachineJARs (>= 1.0), car, randomForest, missForest | graphics, grDevices, stats | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| bartMachineJARs | bartMachineJARs | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1 | NA | R (>= 2.14.0), rJava (>= 0.9-8) | NA | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| base64enc | base64enc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-3 | NA | R (>= 2.9.0) | NA | NA | NA | png | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| bbmle | bbmle | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.23.1 | NA | R (>= 3.0.0), stats4 | stats, numDeriv, lattice, MASS, methods, bdsmatrix, Matrix, mvtnorm | NA | emdbook, rms, ggplot2, RUnit, MuMIn, AICcmodavg, Hmisc, optimx (>= 2013.8.6), knitr, testthat | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| bdsmatrix | bdsmatrix | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-4 | NA | methods, R (>= 2.0.0) | NA | NA | NA | NA | LGPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| beachmat | beachmat | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.0 | NA | NA | methods, DelayedArray, BiocGenerics | NA | testthat, BiocStyle, knitr, rmarkdown, Matrix, devtools | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| beeswarm | beeswarm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.3 | NA | NA | stats, graphics, grDevices, utils | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |
| bench | bench | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.1 | NA | R (>= 3.1) | glue, methods, pillar, profmem, rlang (>= 0.2.0), stats, tibble, utils | NA | covr, dplyr, forcats, ggbeeswarm, ggplot2, ggridges, mockery, parallel, scales, testthat, tidyr (>= 0.8.1), vctrs, withr | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| bestNormalize | bestNormalize | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.0 | NA | R (>= 3.1.0) | LambertW, nortest, dplyr, doParallel, foreach, doRNG, recipes, tibble | NA | knitr, rmarkdown, MASS, testthat, mgcv, parallel | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| bibtex | bibtex | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.2.2 | NA | R (>= 3.0.2) | stringr, utils | NA | testthat | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| biclust | biclust | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.2 | NA | R (>= 2.10), MASS, grid, colorspace, lattice | methods, flexclust, additivityTests, tidyr, ggplot2 | NA | isa2 | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| biocViews | biocViews | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.52.2 | NA | R (>= 3.6.0) | Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager | NA | BiocGenerics, knitr, commonmark | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.2 |
| biomaRt | biomaRt | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.40.5 | NA | methods | utils, XML, RCurl, AnnotationDbi, progress, stringr, httr | NA | annotate, BiocStyle, knitr, rmarkdown, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| biostatUZH | biostatUZH | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8.0 | NA | R (>= 2.15.0), grDevices, graphics, stats, survival (>= 2.35) | boot | NA | cmprsk, lme4, prodlim, psy, xtable, reporttools, Hmisc, surveillance, carData | MASS, ellipse | GPL (>=2) | NA | NA | NA | NA | no | 3.6.2 |
| bit | bit | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-15.2 | NA | R (>= 2.9.2) | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| bit64 | bit64 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-7 | NA | R (>= 3.0.1), bit (>= 1.1-12), utils, methods, stats | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.0 |
| bitops | bitops | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-6 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |
| blob | blob | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.1 | NA | NA | methods, rlang, vctrs (>= 0.2.1) | NA | covr, crayon, pillar (>= 1.2.1), testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| bmp | bmp | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3 | NA | NA | NA | NA | pixmap, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| bookdown | bookdown | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.19 | NA | NA | htmltools (>= 0.3.6), knitr (>= 1.22), rmarkdown (>= 2.0), xfun (>= 0.6), tinytex (>= 0.12) | NA | htmlwidgets, rstudioapi, miniUI, rsconnect (>= 0.4.3), servr (>= 0.13), shiny, testit (>= 0.9), tufte, webshot | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| bootstrap | bootstrap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2019.6 | NA | stats, R (>= 2.10.0) | NA | NA | NA | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| bounceR | bounceR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1 | NA | R (>= 3.4.3) | purrr, furrr, parallel, mboost, strucchange, np, reshape2, ggplot2, mRMRe, dplyr, future | NA | NA | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| brew | brew | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-6 | NA | NA | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | NA | 3.6.1 |
| brglm | brglm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.2 | NA | R (>= 2.6.0), profileModel | NA | NA | MASS | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| broom | broom | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.6 | NA | R (>= 3.1) | backports, dplyr, generics (>= 0.0.2), methods, nlme, purrr, reshape2, stringr, tibble (>= 3.0.0), tidyr | NA | AER, akima, AUC, bbmle, betareg, biglm, binGroup, boot, brms, btergm, car, caret, coda, covr, e1071, emmeans, ergm, gam (>= 1.15), gamlss, gamlss.data, gamlss.dist, geepack, ggplot2, glmnet, gmm, Hmisc, irlba, Kendall, knitr, ks, Lahman, lavaan, lfe, lme4, lmodel2, lmtest, lsmeans, maps, maptools, MASS, Matrix, mclust, mgcv, muhaz, multcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, plyr, poLCA, psych, quantreg, rgeos, rmarkdown, rsample, rstan, rstanarm, sp, speedglm, statnet.common, survey, survival, testthat, tseries, zoo | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| ca | ca | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.71.1 | NA | R (>= 3.0.0) | NA | NA | rgl (>= 0.64-10), vcd | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| caTools | caTools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.18.0 | NA | R (>= 3.6.0) | bitops | NA | MASS, rpart | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| calibrate | calibrate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7.5 | NA | R (>= 3.5.0), MASS | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| callr | callr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.4.3 | NA | NA | processx (>= 3.4.0), R6, utils | NA | cliapp, covr, crayon, fansi, pingr, ps, rprojroot, spelling, testthat, tibble, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| car | car | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0-7 | NA | R (>= 3.5.0), carData (>= 3.0-0) | abind, MASS, mgcv, nnet, pbkrtest (>= 0.4-4), quantreg, grDevices, utils, stats, graphics, maptools, rio, lme4, nlme | NA | alr4, boot, coxme, knitr, leaps, lmtest, Matrix, MatrixModels, rgl (>= 0.93.960), sandwich, SparseM, survival, survey | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| carData | carData | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0-3 | NA | R (>= 3.0) | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| caret | caret | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 6.0-86 | NA | R (>= 3.2.0), lattice (>= 0.20), ggplot2 | foreach, methods, plyr, ModelMetrics (>= 1.2.2.2), nlme, reshape2, stats, stats4, utils, grDevices, recipes (>= 0.1.10), withr (>= 2.0.0), pROC, | NA | BradleyTerry2, e1071, earth (>= 2.2-3), fastICA, gam (>= 1.15), ipred, kernlab, knitr, klaR, MASS, ellipse, mda, mgcv, mlbench, MLmetrics, nnet, party (>= 0.9-99992), pls, proxy, randomForest, RANN, spls, subselect, pamr, superpc, Cubist, testthat (>= 0.9.1), rpart, dplyr, covr | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| caretEnsemble | caretEnsemble | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.1 | NA | R (>= 3.2.0) | methods, pbapply, ggplot2, digest, plyr, lattice, gridExtra, data.table, caret | NA | caTools, testthat, lintr, randomForest, glmnet, rpart, kernlab, nnet, e1071, ipred, pROC, knitr, mlbench, MASS, gbm, klaR, rmarkdown | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| cba | cba | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2-21 | NA | R (>= 2.10), grid, proxy | stats, graphics, grDevices, methods | NA | gclus, colorspace | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| cellranger | cellranger | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | R (>= 3.0.0) | rematch, tibble | NA | covr, testthat (>= 1.0.0), knitr, rmarkdown | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| checkmate | checkmate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.0 | NA | R (>= 3.0.0) | backports (>= 1.1.0), utils | NA | R6, fastmatch, data.table (>= 1.9.8), devtools, ggplot2, knitr, magrittr, microbenchmark, rmarkdown, testthat (>= 0.11.0), tinytest (>= 1.1.0), tibble | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| chron | chron | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3-55 | NA | R (>= 2.12.0) | graphics, stats | NA | scales, ggplot2 | zoo | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| circlize | circlize | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.9 | NA | R (>= 3.0.0), graphics | GlobalOptions (>= 0.1.0), shape, grDevices, utils, stats, colorspace, methods, grid | NA | knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0), gridBase, png | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| classInt | classInt | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-3 | NA | R (>= 2.2) | grDevices, stats, graphics, e1071, class, KernSmooth | NA | spData (>= 0.2.6.2), units, knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| cli | cli | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.2 | NA | R (>= 2.10) | assertthat, crayon (>= 1.3.4), glue, methods, utils, fansi | NA | callr, covr, htmlwidgets, knitr, mockery, rmarkdown, rstudioapi, prettycode (>= 1.1.0), testthat, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| clipr | clipr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7.0 | NA | NA | utils | NA | covr, knitr, rmarkdown, rstudioapi (>= 0.5), testthat (>= 2.0.0) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| clisymbols | clisymbols | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.0 | NA | NA | NA | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| clue | clue | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3-57 | NA | R (>= 3.2.0) | stats, cluster, graphics, methods | NA | e1071, lpSolve (>= 5.5.7), quadprog (>= 1.4-8), relations | RWeka, ape, cba, cclust, flexclust, flexmix, kernlab, mclust, movMF, modeltools | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| cluster | cluster | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1.0 | recommended | R (>= 3.3.0) | graphics, grDevices, stats, utils | NA | MASS, Matrix | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| clusterProfiler | clusterProfiler | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.12.0 | NA | R (>= 3.4.0) | AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7), ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rvcheck, stats, tidyr, utils | NA | AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| clv | clv | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3-2.2 | NA | cluster, class | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| cmprsk | cmprsk | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2-9 | NA | R (>= 3.0.0), survival | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| coda | coda | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.19-3 | NA | R (>= 2.14.0) | lattice | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| coin | coin | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-1 | NA | R (>= 3.4.0), survival | methods, parallel, stats, stats4, utils, libcoin (>= 1.0-0), matrixStats (>= 0.54.0), modeltools (>= 0.2-9), mvtnorm (>= 1.0-5), multcomp | libcoin (>= 1.0-0) | xtable, e1071, vcd, TH.data (>= 1.0-7) | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| colorspace | colorspace | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-1 | NA | R (>= 3.0.0), methods | graphics, grDevices, stats | NA | datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd, tcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg, knitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis, wesanderson | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| combinat | combinat | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-8 | NA | NA | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | NA | 3.6.0 |
| commonmark | commonmark | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7 | NA | NA | NA | NA | curl, testthat, xml2 | NA | BSD_2_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| compare | compare | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2-6 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| config | config | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3 | NA | NA | yaml (>= 2.1.13) | NA | testthat, knitr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| corpcor | corpcor | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.9 | NA | R (>= 3.0.2) | stats | NA | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 | |
| corrplot | corrplot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.84 | NA | NA | NA | NA | knitr, RColorBrewer, testthat | NA | GPL | NA | NA | NA | NA | no | 3.6.1 |
| covr | covr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.5.0 | NA | R (>= 3.1.0), methods | digest, stats, utils, jsonlite, rex, httr, crayon, withr (>= 1.0.2), yaml | NA | R6, knitr, rmarkdown, htmltools, DT (>= 0.2), testthat, rlang, rstudioapi (>= 0.2), xml2 (>= 1.0.0), parallel, memoise, mockery | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| cowplot | cowplot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | R (>= 3.5.0) | ggplot2 (> 2.2.1), grid, gtable, grDevices, methods, rlang, scales, utils | NA | Cairo, covr, dplyr, forcats, gridGraphics (>= 0.4-0), knitr, lattice, magick, maps, PASWR, rmarkdown, testthat (>= 1.0.0), tidyr, vdiffr (>= 0.3.0), VennDiagram | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| cqn | cqn | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.30.0 | NA | R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg | splines | NA | scales, edgeR | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| cr17 | cr17 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.0 | NA | ggplot2 (>= 2.2.1), survival (>= 2.41-3), cmprsk (>= 2.2-7), gridExtra (>= 2.2.1), R (>= 3.3.2) | dplyr (>= 0.5.0), scales (>= 0.4.1), grid (>= 3.3.0), gtable (>= 0.2.0) | NA | knitr, rmarkdown | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| crayon | crayon | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.4 | NA | NA | grDevices, methods, utils | NA | mockery, rstudioapi, testthat, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| crosstalk | crosstalk | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0.1 | NA | NA | htmltools (>= 0.3.6), jsonlite, lazyeval, R6 | NA | shiny, ggplot2, testthat (>= 2.1.0) | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| crrstep | crrstep | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2015-2.1 | NA | cmprsk | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| crul | crul | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9.0 | NA | NA | curl (>= 3.3), R6 (>= 2.2.0), urltools (>= 1.6.0), httpcode (>= 0.2.0), jsonlite, mime | NA | testthat, fauxpas (>= 0.1.0), webmockr (>= 0.1.0), knitr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| cubature | cubature | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.4 | NA | NA | Rcpp | Rcpp | testthat, knitr, mvtnorm, benchr | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| curl | curl | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.3 | NA | R (>= 3.0.0) | NA | NA | spelling, testthat (>= 1.0.0), knitr, jsonlite, rmarkdown, magrittr, httpuv (>= 1.4.4), webutils | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| cutpointr | cutpointr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.2 | NA | R (>= 3.5.0) | gridExtra (>= 2.2.1), foreach (>= 1.4.3), dplyr (>= 0.8.0), tidyr (>= 1.0.0), purrr (>= 0.3.0), tibble (>= 3.0.0), ggplot2 (>= 3.0.0), Rcpp (>= 0.12.12), stats, utils, rlang (>= 0.4.0) | Rcpp | KernSmooth (>= 2.23-15), fANCOVA (>= 0.5-1), testthat (>= 1.0.2), doRNG (>= 1.6), doParallel (>= 1.0.11), knitr, rmarkdown, mgcv (>= 1.8), crayon (>= 1.3.4), registry (>= 0.5-1), pkgmaker(>= 0.31.1), | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| cyclocomp | cyclocomp | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | NA | callr, crayon, desc, remotes, withr | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| d3heatmap | d3heatmap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.1.2 | NA | NA | scales (>= 0.2.5), htmlwidgets, png, base64enc, dendextend (>= 0.18.0), stats, grDevices | NA | shiny, knitr, rmarkdown | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| data.table | data.table | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.12.8 | NA | R (>= 3.1.0) | methods | NA | bit64, curl, R.utils, knitr, xts, nanotime, zoo, yaml | NA | MPL-2.0 | file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| dbplyr | dbplyr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.3 | NA | R (>= 3.1) | assertthat (>= 0.2.0), DBI (>= 1.0.0), dplyr (>= 0.8.0), glue (>= 1.2.0), lifecycle, methods, purrr (>= 0.2.5), R6 (>= 2.2.2), rlang (>= 0.2.0), tibble (>= 1.4.2), tidyselect (>= 0.2.4), utils | NA | bit64, covr, knitr, Lahman, nycflights13, RMariaDB (>= 1.0.2), rmarkdown, RPostgres (>= 1.1.3), RSQLite (>= 2.1.0), testthat (>= 2.0.0) | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| dbscan | dbscan | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-5 | NA | NA | Rcpp (>= 1.0.0), graphics, stats, methods | Rcpp | fpc, microbenchmark, testthat, dendextend, igraph, knitr, DMwR | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| deepnet | deepnet | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2 | NA | NA | NA | NA | NA | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| dendextend | dendextend | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.13.4 | NA | R (>= 3.0.0) | utils, stats, datasets, magrittr (>= 1.0.1), ggplot2, viridis | NA | knitr, rmarkdown, testthat, seriation, colorspace, ape, microbenchmark, gplots, heatmaply, d3heatmap, dynamicTreeCut, pvclust, corrplot, DendSer, MASS, cluster, fpc, circlize (>= 0.2.5), covr | ggdendro, dendroextras, Hmisc, data.table, rpart | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| desc | desc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.0 | NA | R (>= 3.1.0) | assertthat, utils, R6, crayon, rprojroot | NA | covr, testthat, whoami, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| descr | descr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.4 | NA | NA | xtable, utils, grDevices, graphics, stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| desirability | desirability | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1 | NA | NA | stats, graphics, grDevices | NA | lattice | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| devtools | devtools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3.0 | NA | R (>= 3.0.2), usethis (>= 1.6.0) | callr (>= 3.4.3), cli (>= 2.0.2), covr (>= 3.5.0), crayon (>= 1.3.4), desc (>= 1.2.0), digest (>= 0.6.25), DT (>= 0.13), ellipsis (>= 0.3.0), glue (>= 1.4.0), git2r (>= 0.26.1), httr (>= 1.4.1), jsonlite (>= 1.6.1), memoise (>= 1.1.0), pkgbuild (>= 1.0.6), pkgload (>= 1.0.2), rcmdcheck (>= 1.3.3), remotes (>= 2.1.1), rlang (>= 0.4.5), roxygen2 (>= 7.1.0), rstudioapi (>= 0.11), rversions (>= 2.0.1), sessioninfo (>= 1.1.1), stats, testthat (>= 2.3.2), tools, utils, withr (>= 2.1.2) | NA | BiocManager (>= 1.30.10), curl (>= 4.3), foghorn (>= 1.1.5), gmailr (>= 1.0.0), knitr (>= 1.28), lintr (>= 2.0.1), mockery (>= 0.4.2), pingr (>= 2.0.0), MASS, pkgdown (>= 1.5.1), rhub (>= 1.1.1), rmarkdown (>= 2.1), spelling (>= 2.1) | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| diffobj | diffobj | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 3.1.0) | crayon (>= 1.3.2), tools, methods, utils, stats | NA | knitr, rmarkdown, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| digest | digest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.25 | NA | R (>= 3.1.0) | utils | NA | tinytest, knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| diptest | diptest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.75-7 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| doBy | doBy | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.6.5 | NA | R (>= 3.6.0), methods | pbkrtest (>= 0.4-8.1), MASS, Matrix, dplyr, plyr, magrittr, Deriv, tibble, broom | NA | multcomp, geepack, lme4, survival, ggplot2, knitr | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| doParallel | doParallel | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.15 | NA | R (>= 2.14.0), foreach(>= 1.2.0), iterators(>= 1.0.0), parallel, utils | NA | NA | caret, mlbench, rpart, RUnit | compiler | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| doRNG | doRNG | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8.2 | NA | R (>= 3.0.0), foreach, rngtools (>= 1.5) | stats, utils, iterators | NA | doParallel, doMPI, doRedis, rbenchmark, devtools, knitr, bibtex, testthat, pkgmaker (>= 0.31) | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| doSNOW | doSNOW | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.18 | NA | R (>= 2.5.0), foreach(>= 1.2.0), iterators(>= 1.0.0), snow(>= 0.3.0), utils | NA | NA | compiler, RUnit, caret, mlbench, rpart, parallel | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| docker4seq | docker4seq | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3.4 | NA | R (>= 3.0.0) | NA | NA | BiocStyle, knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| dotCall64 | dotCall64 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-0 | NA | R (>= 3.1) | NA | NA | microbenchmark, OpenMPController, RColorBrewer, roxygen2, spam, testthat, | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| downloader | downloader | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4 | NA | NA | utils, digest | NA | testthat | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| dplyr | dplyr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.8.5 | NA | R (>= 3.2.0) | ellipsis, assertthat (>= 0.2.0), glue (>= 1.3.0), magrittr (>= 1.5), methods, pkgconfig, R6, Rcpp (>= 1.0.1), rlang (>= 0.4.0), tibble (>= 2.0.0), tidyselect (>= 0.2.5), utils | BH, plogr (>= 0.2.0), Rcpp (>= 1.0.1) | bit64, callr, covr, crayon (>= 1.3.4), DBI, dbplyr, dtplyr, ggplot2, hms, knitr, Lahman, lubridate, MASS, mgcv, microbenchmark, nycflights13, rmarkdown, RMySQL, RPostgreSQL, RSQLite, testthat, withr, broom, purrr, readr | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| dtplyr | dtplyr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | R (>= 3.2) | crayon, data.table (>= 1.12.4), dplyr (>= 0.8.1), rlang, tibble, tidyselect | NA | bench, covr, knitr, rmarkdown, testthat (>= 2.1.0) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| dtw | dtw | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.21-3 | NA | R (>= 2.10.0), proxy | graphics, grDevices, stats, utils | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| dynamicTreeCut | dynamicTreeCut | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.63-1 | NA | R (>= 2.3.0), stats | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| e1071 | e1071 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7-3 | NA | NA | graphics, grDevices, class, stats, methods, utils | NA | cluster, mlbench, nnet, randomForest, rpart, SparseM, xtable, Matrix, MASS, slam | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| earth | earth | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.1.2 | NA | R (>= 3.4.0), Formula (>= 1.2-3), plotmo (>= 3.5.4), TeachingDemos (>= 2.10) | NA | NA | gam (>= 1.16), mgcv (>= 1.8-26), mda (>= 0.4-10), MASS (>= 7.3-51) | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| edgeR | edgeR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.26.8 | NA | R (>= 3.6.0), limma (>= 3.34.5) | graphics, stats, utils, methods, locfit, Rcpp | Rcpp | AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines | NA | GPL (>=2) | NA | NA | NA | NA | yes | 3.6.2 |
| egg | egg | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.5 | NA | gridExtra (>= 2.3), ggplot2 | gtable, grid, grDevices, utils | NA | knitr, png | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| ellipse | ellipse | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.1 | NA | R (>= 2.0.0),graphics,stats | NA | NA | MASS | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| ellipsis | ellipsis | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 3.2) | rlang (>= 0.3.0) | NA | covr, testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| emdbook | emdbook | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.12 | NA | NA | MASS, lattice, plyr, coda, bbmle | NA | R2jags, ellipse, SuppDists, numDeriv, testthat, rgl | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| enc | enc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.2 | NA | R (>= 3.1) | methods | NA | digest, pillar, readr, rlang, testthat, withr | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| enrichplot | enrichplot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.0 | NA | R (>= 3.4.0) | AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2, ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices, grid, gridExtra, igraph, methods, purrr, RColorBrewer, reshape2, stats, UpSetR, utils | NA | clusterProfiler, dplyr, knitr, org.Hs.eg.db, prettydoc | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| entropy | entropy | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.1 | NA | R (>= 2.15.1) | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 | |
| epiDisplay | epiDisplay | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.5.0.1 | NA | R (>= 2.6.2), foreign, survival, MASS, nnet | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 | |
| europepmc | europepmc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3 | NA | R (>= 3.00) | httr, jsonlite, plyr, dplyr, progress, urltools, purrr, xml2 | NA | testthat, knitr, rmarkdown, ggplot2, readr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| evaluate | evaluate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.14 | NA | R (>= 3.0.2) | methods | NA | testthat, lattice, ggplot2 | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| evtree | evtree | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-8 | NA | R (>= 3.3.0), partykit | NA | NA | Formula, kernlab, lattice, mlbench, multcomp, party, rpart, xtable | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| exactRankTests | exactRankTests | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.8-31 | NA | R (>= 2.4.0), stats, utils | NA | NA | survival | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| ezfun | ezfun | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.3 | NA | R (>= 3.1.0) | NA | NA | knitr, rmarkdown | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| fBasics | fBasics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3042.89.1 | NA | R (>= 2.15.1), timeDate, timeSeries | stats, grDevices, graphics, methods, utils, MASS, spatial, gss, stabledist | NA | akima, RUnit, tcltk | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| factoextra | factoextra | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.7 | NA | R (>= 3.1.2), ggplot2 (>= 2.2.0) | abind, cluster, dendextend, FactoMineR, ggpubr(>= 0.1.5), grid, stats, reshape2, ggrepel, tidyr | NA | ade4, ca, igraph, MASS, knitr, mclust | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| fansi | fansi | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.1 | NA | R (>= 3.1.0) | NA | NA | unitizer, knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| farver | farver | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.3 | NA | NA | NA | NA | testthat (>= 2.1.0), covr | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| fastICA | fastICA | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2-2 | NA | R (>= 3.0.0) | NA | NA | MASS | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| fastmap | fastmap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | NA | NA | NA | testthat (>= 2.1.1) | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| fastmatch | fastmatch | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-0 | NA | NA | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| fgsea | fgsea | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.10.1 | NA | R (>= 3.3), Rcpp | data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), gridExtra, grid, fastmatch, Matrix, utils | Rcpp, BH | testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery | NA | MIT + file LICENCE | NA | NA | NA | NA | yes | 3.6.1 |
| fields | fields | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 10.3 | NA | R (>= 3.0), methods, spam, maps | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| flashClust | flashClust | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.01-2 | NA | R (>= 2.3.0) | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | NA | 3.6.1 |
| flexclust | flexclust | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-0 | NA | R (>= 2.14.0), graphics, grid, lattice, modeltools | methods, parallel, stats, stats4, class | NA | ellipse, clue, cluster, seriation, skmeans | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| flexmix | flexmix | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3-15 | NA | R (>= 2.15.0), lattice | graphics, grid, grDevices, methods, modeltools (>= 0.2-16), nnet, stats, stats4, utils | NA | actuar, codetools, diptest, Ecdat, ellipse, gclus, glmnet, lme4 (>= 1.1), MASS, mgcv (>= 1.8-0), mlbench, multcomp, mvtnorm, SuppDists, survival | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| foghorn | foghorn | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.1 | NA | R (>= 3.1.0) | clisymbols (>= 1.0.0), crayon (>= 1.3.2), curl (>= 2.2), httr (>= 1.2.1), jsonlite (>= 1.5), rlang (>= 0.4.3), rvest (>= 0.3.2), tibble (>= 1.2), xml2 (>= 1.0.0) | NA | covr, dplyr, knitr, progress, rmarkdown, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| fontBitstreamVera | fontBitstreamVera | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.1 | NA | R (>= 3.0.0) | NA | NA | NA | NA | file LICENCE | yes | NA | NA | NA | no | 3.6.1 |
| fontLiberation | fontLiberation | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.0 | NA | R (>= 3.0) | NA | NA | NA | NA | file LICENSE | yes | NA | NA | NA | no | 3.6.1 |
| fontquiver | fontquiver | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.1 | NA | R (>= 3.0.0) | fontBitstreamVera (>= 0.1.0), fontLiberation (>= 0.1.0) | NA | testthat, htmltools | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| forcats | forcats | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.0 | NA | R (>= 3.2) | ellipsis, magrittr, rlang, tibble | NA | covr, ggplot2, testthat, readr, knitr, rmarkdown, dplyr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| foreach | foreach | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.0 | NA | R (>= 2.5.0) | codetools, utils, iterators | NA | randomForest, doMC, doParallel, testthat, knitr, rmarkdown | NA | Apache License (== 2.0) | NA | NA | NA | NA | no | 3.6.2 |
| formatR | formatR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7 | NA | R (>= 3.0.2) | NA | NA | codetools, shiny, testit, rmarkdown, knitr | NA | GPL | NA | NA | NA | NA | no | 3.6.0 |
| fpc | fpc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2-5 | NA | R (>= 2.0) | MASS, cluster, mclust, flexmix, prabclus, class, diptest, robustbase, kernlab, grDevices, graphics, methods, stats, utils, parallel | NA | tclust, pdfCluster, EMMIXskew, mvtnorm | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| freetypeharfbuzz | freetypeharfbuzz | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.5 | NA | R (>= 3.2) | fontquiver | NA | covr, testthat | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| fs | fs | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.1 | NA | R (>= 3.1) | methods | NA | testthat, covr, pillar (>= 1.0.0), tibble (>= 1.1.0), crayon, rmarkdown, knitr, withr, spelling | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| funModeling | funModeling | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.9.3 | NA | R (>= 3.4.0), Hmisc (>= 3.17.1) | ROCR, ggplot2, gridExtra, pander, reshape2, scales, dplyr, lazyeval, utils, RColorBrewer, moments, entropy, cli, stringr | NA | knitr, rmarkdown | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| furrr | furrr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.0 | NA | R (>= 3.2.0), future (>= 1.6.2) | globals (>= 0.10.3), rlang (>= 0.2.0), purrr (>= 0.2.4) | NA | listenv (>= 0.6.0), dplyr (>= 0.7.4), testthat | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.1 |
| futile.logger | futile.logger | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.3 | NA | R (>= 3.0.0) | utils, lambda.r (>= 1.1.0), futile.options | NA | testthat, jsonlite | NA | LGPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| futile.options | futile.options | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | R (>= 2.8.0) | NA | NA | NA | NA | LGPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| future | future | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.17.0 | NA | NA | digest, globals (>= 0.12.5), listenv (>= 0.8.0), parallel, utils | NA | RhpcBLASctl, R.rsp, markdown | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.2 |
| gWidgets | gWidgets | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-54.2 | NA | methods, utils | NA | NA | gWidgetstcltk | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| gam | gam | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.16.1 | NA | stats, splines, foreach | NA | NA | akima | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| gargle | gargle | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.0 | NA | R (>= 3.2) | fs (>= 1.3.1), glue (>= 1.3.0), httr (>= 1.4.0), jsonlite, rlang (>= 0.4.2), stats, withr | NA | covr, knitr, rmarkdown, sodium, spelling, testthat (>= 2.3.2) | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| gbm | gbm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1.5 | NA | R (>= 2.9.0) | gridExtra, lattice, parallel, survival | NA | knitr, pdp, RUnit, splines, viridis | NA | GPL (>= 2) | file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| gclus | gclus | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.2 | NA | R (>= 2.10), cluster | NA | NA | knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| gdata | gdata | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.18.0 | NA | R (>= 2.3.0) | gtools, stats, methods, utils | NA | RUnit | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| gdtools | gdtools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.2 | NA | NA | Rcpp (>= 0.12.12), systemfonts (>= 0.1.1) | Rcpp | htmltools, testthat, fontquiver (>= 0.2.0), curl | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| geepack | geepack | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-1 | NA | R (>= 3.5.0), methods | MASS, broom, magrittr | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.1 |
| genefilter | genefilter | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.66.0 | NA | NA | S4Vectors (>= 0.9.42), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival | NA | class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |
| geneplotter | geneplotter | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.62.0 | NA | R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate | AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils | NA | Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.0 |
| generics | generics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0.2 | NA | R (>= 3.1) | methods | NA | covr, pkgload, testthat, tibble | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| genetics | genetics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.8.1.2 | NA | combinat, gdata, gtools, MASS, mvtnorm | NA | NA | NA | NA | GPL | NA | NA | NA | NA | no | 3.6.0 |
| getopt | getopt | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.20.3 | NA | NA | stats | NA | covr, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| ggbeeswarm | ggbeeswarm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.0 | NA | R (>= 3.0.0), ggplot2 (>= 2.0) | beeswarm, vipor | NA | gridExtra | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| ggbiplot | ggbiplot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.55 | NA | ggplot2, plyr, scales, grid | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| ggdendro | ggdendro | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-20 | NA | NA | MASS, ggplot2(>= 0.9.2) | NA | rpart(>= 4.0-0), tree, testthat, knitr, cluster, scales | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| ggforce | ggforce | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.1 | NA | ggplot2 (>= 3.0.0), R (>= 3.3.0) | Rcpp (>= 0.12.2), grid, scales, MASS, tweenr (>= 0.1.5), gtable, rlang, polyclip, stats, grDevices, tidyselect, withr, utils | Rcpp, RcppEigen | sessioninfo, concaveman, deldir, reshape2, units (>= 0.4-6) | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| ggplot2 | ggplot2 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.3.0 | NA | R (>= 3.2) | digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband, MASS, mgcv, rlang (>= 0.3.0), scales (>= 0.5.0), stats, tibble, withr (>= 2.0.0) | NA | covr, dplyr, ggplot2movies, hexbin, Hmisc, knitr, lattice, mapproj, maps, maptools, multcomp, munsell, nlme, profvis, quantreg, rgeos, rmarkdown, rpart, sf (>= 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 2.1.0), vdiffr (>= 0.3.0) | sp | GPL-2 | file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| ggplot2movies | ggplot2movies | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0.1 | NA | R (>= 2.10.0) | NA | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| ggplotify | ggplotify | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0.5 | NA | R (>= 3.4.0) | ggplot2, graphics, grDevices, grid, gridGraphics, rvcheck | NA | colorspace, cowplot, ggimage, knitr, lattice, prettydoc, vcd | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.2 |
| ggpubr | ggpubr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 3.1.0), ggplot2 | ggrepel, grid, ggsci, stats, utils, tidyr, purrr, dplyr (>= 0.7.1), cowplot, ggsignif, scales, gridExtra, glue, polynom, rlang, rstatix (>= 0.4.0), tibble, magrittr | NA | grDevices, knitr, RColorBrewer, gtable | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| ggraph | ggraph | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.2 | NA | R (>= 2.10), ggplot2 (>= 3.0.0) | Rcpp (>= 0.12.2), dplyr, ggforce (>= 0.3.1), grid, igraph (>= 1.0.0), scales, MASS, digest, gtable, ggrepel, utils, stats, viridis, rlang, tidygraph, graphlayouts (>= 0.5.0) | Rcpp | network, knitr, rmarkdown, purrr, tibble, seriation, deldir, gganimate | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| ggraptR | ggraptR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2 | NA | dplyr (>= 0.7.5), ggplot2 (>= 2.2.0), pacman (>= 0.4.6), purrr(>= 0.2.4), shiny (>= 0.12.2) | NA | NA | knitr | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| ggrepel | ggrepel | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.8.2 | NA | R (>= 3.0.0), ggplot2 (>= 2.2.0) | grid, Rcpp, scales (>= 0.3.0) | Rcpp | knitr, rmarkdown, testthat, gridExtra, devtools, prettydoc | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| ggridges | ggridges | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.2 | NA | R (>= 3.2) | ggplot2 (>= 3.0.0), grid (>= 3.0.0), plyr (>= 1.8.0), scales (>= 0.4.1), withr (>= 2.1.1) | NA | covr, dplyr, patchwork, ggplot2movies, forcats, knitr, rmarkdown, testthat, vdiffr | NA | GPL-2 | file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| ggsci | ggsci | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.9 | NA | R (>= 3.0.2) | grDevices, scales, ggplot2 (>= 2.0.0) | NA | knitr, rmarkdown, gridExtra, reshape2 | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| ggsignif | ggsignif | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.0 | NA | NA | ggplot2 (>= 2.0.0) | NA | testthat, knitr, rmarkdown | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| ggthemes | ggthemes | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.2.0 | NA | R (>= 3.3.0) | ggplot2 (>= 3.0.0), graphics, grid, methods, purrr, scales, stringr, tibble | NA | dplyr, covr, extrafont, glue, knitr, lattice, lintr, maps, mapproj, pander, rlang, rmarkdown, spelling, testthat, tidyr, vdiffr, withr | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| gh | gh | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | NA | cli, ini, jsonlite, httr (>= 1.2) | NA | covr, keyring, pingr, testthat, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| git2r | git2r | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.27.1 | NA | R (>= 3.1) | graphics, utils | NA | getPass | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| gld | gld | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.6.2 | NA | NA | stats, graphics, e1071, lmom | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 | |
| glmnet | glmnet | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.0 | NA | R (>= 3.6.0), Matrix (>= 1.0-6) | methods, utils, foreach, shape | NA | survival, knitr, lars, testthat | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| globals | globals | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.12.5 | NA | R (>= 3.1.2) | codetools | NA | NA | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.1 |
| glue | glue | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.1 | NA | R (>= 3.1) | methods | NA | testthat, covr, magrittr, crayon, knitr, rmarkdown, DBI, RSQLite, R.utils, forcats, microbenchmark, rprintf, stringr, ggplot2, dplyr, withr, vctrs (>= 0.3.0) | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| gmailr | gmailr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | R (>= 3.0.0) | base64enc, crayon, gargle, httr, jsonlite, lifecycle, magrittr, mime, rematch2 | NA | covr, knitr, methods, sodium, rmarkdown, testthat, xml2 | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| goftest | goftest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2-2 | NA | R (>= 3.3) | stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| gower | gower | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.1 | NA | NA | NA | NA | tinytest (>= 0.9.3), | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| gplots | gplots | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0.3 | NA | R (>= 3.0) | gtools, gdata, stats, caTools, KernSmooth | NA | grid, MASS, knitr | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| gpuR | gpuR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.3 | NA | R (>= 3.0.2), methods, utils | Rcpp (>= 0.12.15), assertive | Rcpp (>= 0.12.15), RcppEigen (>= 0.3.3.4.0), RViennaCL (>= 1.7.1.7), BH | testthat, knitr | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| graph | graph | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.62.0 | NA | R (>= 2.10), methods, BiocGenerics (>= 0.13.11) | stats, stats4, utils | NA | SparseM (>= 0.36), XML, RBGL, RUnit, cluster | Rgraphviz | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| graphlayouts | graphlayouts | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7.0 | NA | R (>= 3.2.0) | igraph, Rcpp | Rcpp, RcppArmadillo | oaqc, testthat, ggraph, ggplot2, knitr, rmarkdown | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| gridExtra | gridExtra | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3 | NA | NA | gtable, grid, grDevices, graphics, utils | NA | ggplot2, egg, lattice, knitr, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| gridGraphics | gridGraphics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5-0 | NA | grid, graphics | grDevices | NA | magick (>= 1.3), pdftools (>= 1.6) | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| gss | gss | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2-0 | NA | R (>= 3.0.0), stats | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| gsubfn | gsubfn | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7 | NA | proto | NA | NA | boot, chron, grid, lattice, quantreg, svUnit, tcltk, zoo | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| gtable | gtable | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 3.0) | grid | NA | covr, testthat, knitr, rmarkdown, ggplot2, profvis | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| gtools | gtools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.8.2 | NA | methods, stats, utils | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| haven | haven | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2.0 | NA | R (>= 3.2) | forcats (>= 0.2.0), hms, Rcpp (>= 0.11.4), readr (>= 0.1.0), rlang (>= 0.4.0), tibble, tidyselect | Rcpp | covr, fs, knitr, rmarkdown, testthat, pillar (>= 1.4.0), cli, crayon | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| heatmaply | heatmaply | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | R (>= 3.0.0), plotly (>= 4.7.1), viridis | ggplot2 (>= 2.2.0), dendextend (>= 1.12.0), magrittr (>= 1.0.1), reshape2, scales, seriation, utils, stats, grDevices, methods, colorspace, RColorBrewer, htmlwidgets, webshot, assertthat, egg | NA | knitr, covr, gplots, tidyselect, rmarkdown, testthat | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| hexbin | hexbin | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.28.1 | NA | R (>= 2.0.1), methods | lattice, grid, graphics, grDevices, stats, utils | NA | marray, affy, Biobase, limma, knitr | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| highlight | highlight | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.0 | NA | R (>= 3.2) | grDevices, tools | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.1 |
| highr | highr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.8 | NA | R (>= 3.2.3) | NA | NA | knitr, testit | NA | GPL | NA | NA | NA | NA | no | 3.6.0 |
| hmeasure | hmeasure | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-2 | NA | R (>= 2.10) | NA | NA | MASS, class, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| hms | hms | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.3 | NA | NA | methods, pkgconfig, rlang, vctrs (>= 0.2.1) | NA | crayon, lubridate, pillar (>= 1.1.0), testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| htmlTable | htmlTable | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.13.3 | NA | NA | stringr, knitr (>= 1.6), magrittr (>= 1.5), methods, checkmate, htmlwidgets, htmltools, rstudioapi (>= 0.6) | NA | testthat, XML, xtable, ztable, Hmisc, reshape, rmarkdown, pander, chron, lubridate, tibble, tidyr (>= 0.7.2), dplyr (>= 0.7.4) | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| htmltools | htmltools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.0 | NA | R (>= 2.14.1) | utils, digest, Rcpp, rlang | Rcpp | markdown, testthat, withr | knitr | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| htmlwidgets | htmlwidgets | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.1 | NA | NA | grDevices, htmltools (>= 0.3), jsonlite (>= 0.9.16), yaml | NA | knitr (>= 1.8) | shiny (>= 1.1) | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| httpcode | httpcode | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | NA | NA | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| httpuv | httpuv | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.2 | NA | R (>= 2.15.1) | Rcpp (>= 0.11.0), utils, R6, promises, later (>= 0.8.0) | Rcpp, BH, later | testthat, callr, curl, websocket | NA | GPL (>= 2) | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| httr | httr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.1 | NA | R (>= 3.2) | curl (>= 3.0.0), jsonlite, mime, openssl (>= 0.8), R6 | NA | covr, httpuv, jpeg, knitr, png, readr, rmarkdown, testthat (>= 0.8.0), xml2 | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| hunspell | hunspell | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0 | NA | R (>= 3.0.2) | Rcpp, digest | Rcpp (>= 0.12.12) | spelling, testthat, pdftools, janeaustenr, wordcloud2, knitr, stopwords, rmarkdown | NA | GPL-2 | LGPL-2.1 | MPL-1.1 | NA | NA | NA | NA | yes | 3.6.1 |
| hwriter | hwriter | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.2 | NA | R (>= 2.6.0) | NA | NA | NA | NA | LGPL-2.1 | NA | NA | NA | NA | no | 3.6.1 |
| igraph | igraph | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.5 | NA | methods | graphics, grDevices, magrittr, Matrix, pkgconfig (>= 2.0.0), stats, utils | NA | ape, digest, graph, igraphdata, rgl, scales, stats4, tcltk, testthat, withr | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| imager | imager | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.42.3 | NA | R (>= 2.10.0),magrittr | Rcpp (>= 0.11.5),methods,stringr,png,jpeg,readbitmap,grDevices,purrr,downloader,igraph | Rcpp | knitr, rmarkdown,ggplot2,dplyr,scales, testthat,OpenMPController,raster,spatstat, magick,Cairo | NA | LGPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| import | import | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | NA | NA | NA | knitr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| imputeMissings | imputeMissings | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0.3 | NA | NA | randomForest,stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| inTrees | inTrees | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2 | NA | NA | RRF, arules, gbm, xtable, xgboost, data.table, methods | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.0 |
| inflection | inflection | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.5 | NA | NA | parallel, stats, graphics, grDevices | NA | knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| influenceR | influenceR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.0 | NA | R (>= 3.2.0) | igraph (>= 1.0.1), Matrix (>= 1.1-4), methods, utils | NA | testthat | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| ini | ini | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.1 | NA | NA | NA | NA | testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| inum | inum | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-1 | NA | R (>= 3.3.0) | stats, libcoin (>= 1.0-0) | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| ipred | ipred | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-9 | NA | R (>= 2.10) | rpart (>= 3.1-8), MASS, survival, nnet, class, prodlim | NA | mvtnorm, mlbench, TH.data | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |
| irlba | irlba | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3.3 | NA | Matrix | stats, methods | Matrix | NA | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| isoband | isoband | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.1 | NA | NA | Rcpp, grid, utils | Rcpp, testthat | covr, ggplot2, knitr, magick, microbenchmark, rmarkdown, sf, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| iterators | iterators | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.12 | NA | R (>= 2.5.0), utils | NA | NA | RUnit, foreach | NA | Apache License (== 2.0) | NA | NA | NA | NA | no | 3.6.1 |
| itertools | itertools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-3 | NA | R (>= 2.14.0), iterators(>= 1.0.0) | parallel | NA | foreach | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| janitor | janitor | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.1 | NA | R (>= 3.1.2) | dplyr (>= 0.7.0), lifecycle, lubridate, magrittr, purrr, rlang, stringi, stringr, snakecase (>= 0.9.2), tidyselect (>= 1.0.0), tidyr (>= 0.7.0) | NA | knitr, rmarkdown, sf, testthat, tibble, tidygraph | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| jomo | jomo | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.7-0 | NA | NA | stats, lme4, survival, MASS, ordinal | NA | mitml | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| jpeg | jpeg | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-8.1 | NA | R (>= 2.9.0) | NA | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| jsonlite | jsonlite | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.1 | NA | methods | NA | NA | httr, curl, plyr, testthat, knitr, rmarkdown, R.rsp, sp | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| kableExtra | kableExtra | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | R (>= 3.1.0) | knitr (>= 1.16), magrittr, stringr (>= 1.0), xml2 (>= 1.1.1), rvest, rmarkdown (>= 1.6.0), readr, scales, viridisLite, stats, grDevices, htmltools, rstudioapi, glue, tools, webshot, digest | NA | testthat, magick, formattable, dplyr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| keras | keras | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2.5.0 | NA | R (>= 3.2) | generics (>= 0.0.1), reticulate (>= 1.10), tensorflow (>= 2.0.0), tfruns (>= 1.0), magrittr, zeallot, methods, R6 | NA | ggplot2, testthat (>= 2.1.0), knitr, rmarkdown, tfdatasets, jpeg | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| kernlab | kernlab | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-29 | NA | R (>= 2.10) | methods, stats, grDevices, graphics | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| klaR | klaR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6-15 | NA | R (>= 2.10.0), MASS | combinat, questionr, grDevices, stats, utils, graphics | NA | scatterplot3d (>= 0.3-22), som, mlbench, rpart, e1071 | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| km.ci | km.ci | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5-2 | NA | R (>= 1.8.0), survival, stats | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | NA | 3.6.0 |
| knitcitations | knitcitations | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.10 | NA | R (>= 3.0) | RefManageR (>= 0.8.2), digest, httr (>= 0.3), methods, utils | NA | testthat, knitr (>= 1.6) | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| knitr | knitr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.28 | NA | R (>= 3.2.3) | evaluate (>= 0.10), highr, markdown, stringr (>= 0.6), yaml (>= 2.1.19), methods, xfun, tools | NA | formatR, testit, digest, rgl (>= 0.95.1201), codetools, rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice (>= 0.10), tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1), magick, png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>= 0.4-1), showtext, tibble, sass, styler (>= 1.2.0) | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| ks | ks | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.11.7 | NA | R (>= 2.10.0) | FNN (>= 1.1), kernlab, KernSmooth (>= 2.22), Matrix, mclust, mgcv, multicool, mvtnorm (>= 1.0-0) | NA | maps, MASS, misc3d (>= 0.4-0), OceanView, oz, rgl (>= 0.66) | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| labeling | labeling | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3 | NA | NA | NA | NA | NA | NA | MIT + file LICENSE | Unlimited | NA | NA | NA | NA | no | 3.6.0 |
| labelled | labelled | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3.1 | NA | NA | haven (>= 2.1.0), dplyr, stats | NA | testthat, knitr, rmarkdown, questionr, snakecase | memisc | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| laeken | laeken | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.1 | NA | R (>= 3.2.0) | boot, MASS | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| lamW | lamW | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.0 | NA | R (>= 3.0.2) | Rcpp, RcppParallel (>= 4.3.20) | Rcpp, RcppParallel (>= 4.3.20) | testthat | NA | BSD_2_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| lambda.r | lambda.r | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.4 | NA | R (>= 3.0.0) | formatR | NA | testit | NA | LGPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| lars | lars | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2 | NA | R (>= 2.10) | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| later | later | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | NA | Rcpp (>= 0.12.9), rlang | Rcpp, BH | knitr, rmarkdown, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| latticeExtra | latticeExtra | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6-29 | NA | R (>= 3.6.0), lattice | grid, stats, utils, grDevices, png, jpeg, RColorBrewer | NA | maps, mapproj, deldir, tripack, quantreg, zoo, MASS, mgcv | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| lava | lava | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.7 | NA | R (>= 3.0) | grDevices, graphics, methods, numDeriv, stats, survival, SQUAREM, utils | NA | KernSmooth, Matrix, Rgraphviz, data.table, ellipse, fields, foreach, geepack, gof (>= 0.9), graph, igraph (>= 0.6), lava.tobit (>= 0.4.7), lme4, mets (>= 1.1), nlme, optimx, polycor, quantreg, rgl, testthat (>= 0.11), visNetwork, zoo | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| lava.tobit | lava.tobit | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5 | NA | lava (>= 1.5), mets (>= 1.2.2), mvtnorm, survival | NA | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| lavaan | lavaan | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6-6 | NA | R(>= 3.4) | methods, stats4, stats, utils, graphics, MASS, mnormt, pbivnorm, numDeriv | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| lazyeval | lazyeval | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.2 | NA | R (>= 3.1.0) | NA | NA | knitr, rmarkdown (>= 0.2.65), testthat, covr | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| leaps | leaps | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.1 | NA | NA | NA | biglm | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 | |
| libcoin | libcoin | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-5 | NA | R (>= 3.4.0) | stats, mvtnorm | mvtnorm | coin | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| lifecycle | lifecycle | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.0 | NA | R (>= 3.2) | glue, rlang (>= 0.4.0) | NA | covr, crayon, knitr, rmarkdown, testthat (>= 2.1.0) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| limma | limma | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.40.6 | NA | R (>= 3.6.0) | grDevices, graphics, stats, utils, methods | NA | affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn | NA | GPL (>=2) | NA | NA | NA | NA | yes | 3.6.1 |
| lintr | lintr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.1 | NA | R (>= 3.2) | rex, crayon, codetools, cyclocomp, testthat (>= 2.2.1), digest, rstudioapi (>= 0.2), httr (>= 1.2.1), jsonlite, knitr, stats, utils, xml2 (>= 1.0.0), xmlparsedata (>= 1.0.3) | NA | rmarkdown, mockery | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| listenv | listenv | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.8.0 | NA | R (>= 3.1.2) | NA | NA | R.utils, R.rsp, markdown | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.1 |
| lm.beta | lm.beta | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5-1 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| lme4 | lme4 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-23 | NA | R (>= 3.2.0), Matrix (>= 1.2-1), methods, stats | graphics, grid, splines, utils, parallel, MASS, lattice, boot, nlme (>= 3.1-123), minqa (>= 1.1.15), nloptr (>= 1.0.4), statmod | Rcpp (>= 0.10.5), RcppEigen | knitr, rmarkdown, PKPDmodels, MEMSS, testthat (>= 0.8.1), ggplot2, mlmRev, optimx (>= 2013.8.6), gamm4, pbkrtest, HSAUR2, numDeriv, car, dfoptim | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| lmom | lmom | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.8 | NA | R (>= 3.0.0) | stats, graphics | NA | NA | NA | Common Public License Version 1.0 | NA | NA | NA | NA | yes | 3.6.1 |
| lmtest | lmtest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-37 | NA | R (>= 3.0.0), stats, zoo | graphics | NA | car, strucchange, sandwich, dynlm, stats4, survival, AER | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| locfit | locfit | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5-9.4 | NA | R (>= 3.5.0) | lattice | NA | interp, gam | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| logcondens | logcondens | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1.5 | NA | R (>= 2.10) | ks, graphics, stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| lsr | lsr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5 | NA | NA | NA | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| lubridate | lubridate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7.8 | NA | methods, R (>= 3.2) | generics, Rcpp (>= 0.12.13) | Rcpp | covr, knitr, testthat | chron, timeDate, tis, zoo | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| mRMRe | mRMRe | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1.0 | NA | survival, igraph, methods | NA | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| magick | magick | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3 | NA | NA | Rcpp (>= 0.12.12), magrittr, curl | Rcpp | av (>= 0.3), spelling, jsonlite, methods, knitr, rmarkdown, rsvg, webp, pdftools, ggplot2, raster, rgdal, gapminder, IRdisplay, tesseract (>= 2.0), gifski | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| magrittr | magrittr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5 | NA | NA | NA | NA | testthat, knitr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| manipulateWidget | manipulateWidget | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.10.1 | NA | NA | shiny (>= 1.0.3), miniUI, htmltools, htmlwidgets, knitr, methods, tools, base64enc, grDevices, codetools, webshot | NA | dygraphs, leaflet, plotly, xts, rmarkdown, testthat, covr | NA | GPL (>= 2) | file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| mapdata | mapdata | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3.0 | NA | R (>= 2.14.0), maps (>= 2.0-7) | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| mapproj | mapproj | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.7 | NA | R (>= 3.0.0), maps (>= 2.3-0) | stats, graphics | NA | NA | NA | Lucent Public License | NA | NA | NA | NA | yes | 3.6.2 |
| maps | maps | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.3.0 | NA | R (>= 3.0.0) | graphics, utils | NA | mapproj (>= 1.2-0), mapdata (>= 2.3.0), sp, maptools, rnaturalearth | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| maptools | maptools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-1 | NA | R (>= 2.10), sp (>= 1.0-11) | foreign (>= 0.8), methods, grid, lattice, stats, utils, grDevices | NA | rgeos (>= 0.1-8), spatstat (>= 1.60), PBSmapping, maps, RColorBrewer, raster, polyclip, spatstat.utils | gpclib | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| markdown | markdown | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1 | NA | R (>= 2.11.1) | utils, xfun, mime (>= 0.3) | NA | knitr, RCurl | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| matlab | matlab | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.2 | NA | R (>= 2.15) | methods | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| matrixStats | matrixStats | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.56.0 | NA | R (>= 2.12.0) | NA | NA | base64enc, ggplot2, knitr, microbenchmark, R.devices, R.rsp | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.2 |
| maxstat | maxstat | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7-25 | NA | R (>= 1.7.0) | exactRankTests(>= 0.8-23), mvtnorm(>= 0.5-10), stats, graphics | NA | TH.data, survival | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |
| mboost | mboost | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.9-2 | NA | R (>= 3.2.0), methods, stats, parallel, stabs (>= 0.5-0) | Matrix, survival, splines, lattice, nnls, quadprog, utils, graphics, grDevices, partykit (>= 1.2-1) | NA | TH.data, MASS, fields, BayesX, gbm, mlbench, RColorBrewer, rpart (>= 4.0-3), randomForest, nnet, testthat (>= 0.10.0), kangar00 | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| mclust | mclust | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.4.6 | NA | R (>= 3.0) | stats, utils, graphics, grDevices | NA | knitr (>= 1.12), rmarkdown (>= 0.9), mix (>= 1.0), geometry (>= 0.3-6), MASS | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| mda | mda | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5 | NA | R (>= 3.5.0), stats, class | NA | NA | earth, testthat | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| memisc | memisc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.99.22 | NA | R (>= 3.3.0), lattice, stats, methods, utils, MASS | grid, repr, data.table | NA | splines, knitr, rmarkdown, sandwich | AER, car, eha, lme4, ordinal, simex, tibble, haven | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| memoise | memoise | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | NA | digest (>= 0.6.3) | NA | testthat, aws.s3, httr, covr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| mets | mets | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.7.1 | NA | R (>= 3.5), timereg (>= 1.9.4), lava (>= 1.6.6) | mvtnorm, numDeriv, compiler, Rcpp, splines, survival (>= 2.43-1), | Rcpp, RcppArmadillo, mvtnorm | prodlim, testthat (>= 0.11), ucminf, R.rsp (>= 0.40) | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| mgcv | mgcv | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8-31 | recommended | R (>= 2.14.0), nlme (>= 3.1-64) | methods, stats, graphics, Matrix, splines, utils | NA | parallel, survival, MASS | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| miRNAselector | miRNAselector | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.0 | NA | NA | dplyr, remotes, devtools, BiocManager, plyr, epiDisplay, rsq, MASS, caret, pROC, ggplot2, DMwR, ROSE, gridExtra, gplots, stringr, data.table, doParallel, Boruta, spFSR, varSelRF, My.stepwise, psych, C50, randomForest, nnet, reticulate, stargazer, ggrepel, classInt, plotly, keras, cutpointr, naniar, visdat, imputeMissings, foreach, deepnet, snow, calibrate, networkD3, VennDiagram, RSNNS, kernlab, car, PairedData, profileR, xgboost, kableExtra, doSNOW, curl, rJava, mice, MatchIt, cluster | NA | knitr, rmarkdown, | NA | License: MIT + file LICENSE | NA | NA | NA | NA | NA | 3.6.2 |
| miRNAtap | miRNAtap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.18.0 | NA | R (>= 3.3.0), AnnotationDbi | DBI, RSQLite, stringr, sqldf, plyr, methods | NA | topGO, org.Hs.eg.db, miRNAtap.db, testthat | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| miRNAtap.db | miRNAtap.db | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.99.10 | NA | miRNAtap | AnnotationDbi, DBI, RSQLite, miRNAtap | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| mice | mice | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.9.0 | NA | R (>= 2.10.0) | broom, dplyr, graphics, lattice, methods, stats, tidyr, utils | Rcpp | knitr, lme4, MASS, mitml, miceadds, nnet, pan, randomForest, rmarkdown, rpart, survival, testthat, lmtest | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| microbenchmark | microbenchmark | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-7 | NA | NA | graphics, stats | NA | ggplot2, multcomp, RUnit | NA | BSD_2_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| mime | mime | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9 | NA | NA | tools | NA | NA | NA | GPL | NA | NA | NA | NA | yes | 3.6.2 |
| miniUI | miniUI | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.1.1 | NA | NA | shiny (>= 0.13), htmltools (>= 0.3), utils | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| minqa | minqa | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.4 | NA | NA | Rcpp (>= 0.9.10) | Rcpp | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.0 |
| missForest | missForest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4 | NA | randomForest,foreach,itertools | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| mitml | mitml | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3-7 | NA | NA | pan, jomo, haven, grDevices, graphics, stats, utils | NA | mice, miceadds, Amelia, lme4, nlme, geepack, survival, knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| mixOmics | mixOmics | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 6.8.5 | NA | R (>= 3.5.0), MASS, lattice, ggplot2 | igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, utils | NA | BiocStyle, knitr, rmarkdown, testthat, rgl | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| mlbench | mlbench | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1-1 | NA | R (>= 2.10) | NA | NA | lattice | NA | GPL-2 | NA | NA | NA | NA | NA | 3.6.1 |
| mlr | mlr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.17.1 | NA | ParamHelpers (>= 1.10), R (>= 3.0.2) | backports (>= 1.1.0), BBmisc (>= 1.11), checkmate (>= 1.8.2), data.table (>= 1.12.4), ggplot2, methods, parallelMap (>= 1.3), stats, stringi, survival, utils, XML | NA | ada, adabag, bartMachine, batchtools, brnn, bst, C50, care, caret (>= 6.0-57), class, clue, cluster, ClusterR, clusterSim (>= 0.44-5), cmaes, cowplot, CoxBoost, crs, Cubist, deepnet, DiceKriging, DiscriMiner, e1071, earth, elasticnet, emoa, evtree, extraTrees, fda.usc, FDboost, FNN, forecast (>= 8.3), fpc, frbs, FSelector, FSelectorRcpp (>= 0.2.1), gbm, GenSA, ggpubr, glmnet, GPfit, h2o (>= 3.6.0.8), Hmisc, hrbrthemes, irace (>= 2.0), kernlab, kknn, klaR, knitr, laGP, LiblineaR, lintr (>= 1.0.0.9001), MASS, mboost, mco, mda, memoise, mlbench, mldr, mlrMBO, mmpf, modeltools, mRMRe, neuralnet, nnet, nodeHarvest (>= 0.7-3), numDeriv, pamr, pander, party, penalized (>= 0.9-47), pls, PMCMR (>= 4.1), praznik (>= 5.0.0), randomForest, randomForestSRC (>= 2.7.0), ranger (>= 0.8.0), rappdirs, refund, rex, rFerns, rgenoud, rknn, rmarkdown, ROCR, rotationForest, rpart, RRF, rrlda, rsm, RSNNS, rucrdtw, RWeka, sda, sf, smoof, sparseLDA, stepPlr, survAUC, svglite, SwarmSVM, testthat, tgp, TH.data, tidyr, tsfeatures, vdiffr, wavelets, xgboost (>= 0.7) | NA | BSD_2_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| mnormt | mnormt | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5-7 | NA | R (>= 2.2.0) | NA | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| mockery | mockery | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.2 | NA | NA | testthat | NA | knitr, rmarkdown (>= 1.0), R6 | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| mockr | mockr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1 | NA | NA | lazyeval | NA | testthat, covr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| modelr | modelr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.7 | NA | R (>= 3.2) | broom, dplyr, magrittr, purrr (>= 0.2.2), rlang (>= 0.2.0), tibble, tidyr (>= 0.8.0), tidyselect | NA | compiler, covr, ggplot2, testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| modeltools | modeltools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2-23 | NA | stats, stats4 | methods | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| moments | moments | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.14 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| mstate | mstate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.12 | NA | survival (>= 3.1) | RColorBrewer | NA | cmprsk | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| multcomp | multcomp | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-13 | NA | stats, graphics, mvtnorm (>= 1.0-10), survival (>= 2.39-4), TH.data (>= 1.0-2) | sandwich (>= 2.3-0), codetools | NA | lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS, foreign, xtable, lmtest, coxme (>= 2.2-1), SimComp, ISwR, tram (>= 0.2-5) | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| multicool | multicool | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-11 | NA | methods, Rcpp (>= 0.11.2) | NA | Rcpp | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| munsell | munsell | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.0 | NA | NA | colorspace, methods | NA | ggplot2, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| mvtnorm | mvtnorm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-0 | NA | R(>= 3.5.0) | stats, methods | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| mxnet | mxnet | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.0 | NA | R (>= 3.4.4) | methods, Rcpp (>= 0.12.1), DiagrammeR (>= 0.9.0), visNetwork (>= 1.0.3), data.table, jsonlite, magrittr, stringr | Rcpp | testthat, mlbench, knitr, rmarkdown, imager, covr | NA | Apache License (== 2.0) | NA | NA | NA | NA | NA | 3.6.1 |
| naniar | naniar | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.1 | NA | R (>= 3.1.2) | dplyr, ggplot2, purrr, tidyr, tibble (>= 2.0.0), magrittr, stats, visdat, rlang, forcats, viridis, glue, UpSetR | NA | knitr, rmarkdown, testthat (>= 2.1.0), rpart, rpart.plot, covr, gridExtra, wakefield, vdiffr, here, simputation, imputeTS, gdtools, Hmisc, spelling | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| networkD3 | networkD3 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4 | NA | R (>= 3.0.0) | htmlwidgets (>= 0.3.2), igraph, magrittr | NA | htmltools (>= 0.2.6), jsonlite, | knitr, shiny | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.2 |
| neuralnet | neuralnet | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.44.2 | NA | R (>= 2.9.0) | grid, MASS, grDevices, stats, utils, Deriv | NA | testthat | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| nloptr | nloptr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.2.1 | NA | NA | NA | NA | testthat (>= 0.8.1), knitr, rmarkdown, inline (>= 0.3.14) | NA | LGPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| nnls | nnls | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | NA | 3.6.0 |
| nor1mix | nor1mix | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-0 | NA | NA | stats, graphics | NA | cluster | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| nortest | nortest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-4 | NA | NA | stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| np | np | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.60-10 | NA | NA | boot, cubature, methods, quadprog, quantreg, stats | NA | MASS | NA | GPL | NA | NA | NA | NA | yes | 3.6.2 |
| numDeriv | numDeriv | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2016.8-1.1 | NA | R (>= 2.11.1) | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| nycflights13 | nycflights13 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | R (>= 3.2) | tibble | NA | dplyr | NA | CC0 | NA | NA | NA | NA | no | 3.6.1 |
| olsrr | olsrr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.3 | NA | R(>= 3.3) | car, data.table, ggplot2, goftest, graphics, gridExtra, nortest, Rcpp, stats, utils | Rcpp | covr, descriptr, knitr, rmarkdown, testthat, vdiffr, xplorerr | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| openintro | openintro | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7.1 | NA | graphics, grDevices, stats, utils, R (>= 2.10) | NA | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| openssl | openssl | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.1 | NA | NA | askpass | NA | testthat, digest, knitr, rmarkdown, jsonlite, jose, sodium | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| openxlsx | openxlsx | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.1.5 | NA | R (>= 3.3.0) | grDevices, methods, Rcpp, stats, utils, zip, stringi | Rcpp | knitr, testthat, roxygen2 | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| optimx | optimx | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2020-4.2 | NA | NA | numDeriv | NA | knitr, rmarkdown, setRNG, BB, ucminf, minqa, dfoptim, lbfgsb3c, lbfgs, subplex | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| optparse | optparse | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.6 | NA | R (>= 2.9.0) | methods, getopt (>= 1.20.2) | NA | covr, knitr (>= 1.15.19), stringr, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| ordinal | ordinal | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2019.12-10 | NA | R (>= 2.13.0), stats, methods | ucminf, MASS, Matrix, numDeriv | NA | lme4, nnet, xtable, testthat (>= 0.8), tools | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| ordinalNet | ordinalNet | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.7 | NA | NA | stats, graphics | NA | testthat (>= 1.0.2), MASS (>= 7.3-45), glmnet (>= 2.0-5), penalized (>= 0.9-50), glmnetcr (>= 1.0.3), VGAM (>= 1.0-3), rms (>= 5.1-0) | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| org.Hs.eg.db | org.Hs.eg.db | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.8.2 | NA | R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1) | methods, AnnotationDbi | NA | DBI, annotate, RUnit | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| oro.dicom | oro.dicom | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.3 | NA | R (>= 2.14.0) | utils, oro.nifti (>= 0.4.0) | NA | testthat, hwriter | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| oro.nifti | oro.nifti | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.10.1 | NA | R (>= 2.14.0) | stats, bitops, splines, graphics, grDevices, methods, utils, abind, RNifti (>= 0.9.0) | NA | XML, testthat, covr, knitr, rmarkdown | dcemriS4, fmri, oro.dicom | BSD_3_clause + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| pROC | pROC | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.16.2 | NA | R (>= 2.14) | methods, plyr, Rcpp (>= 0.11.1) | Rcpp | microbenchmark, tcltk, MASS, logcondens, doParallel, testthat, vdiffr, ggplot2 | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.2 |
| pacman | pacman | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.1 | NA | R (>= 3.5.0) | remotes, methods, stats, utils | NA | BiocManager, knitr, lattice, testthat (>= 0.9.0), XML | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| pamr | pamr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.56.1 | NA | R (>= 2.10), cluster, survival | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| pan | pan | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6 | NA | NA | NA | NA | mitools, lme4 | NA | GPL-3 | NA | no | NA | NA | yes | 3.6.0 |
| pander | pander | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.3 | NA | R (>= 2.15.0) | grDevices, graphics, methods, utils, stats, digest, tools, Rcpp | Rcpp | grid, lattice, ggplot2 (>= 0.9.2), sylly, sylly.en, futile.logger, survival, microbenchmark, zoo, nlme, descr, MASS, knitr, rmarkdown, tables, reshape, memisc, Epi, randomForest, tseries, gtable, rms, forecast, data.table | NA | AGPL-3 | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| parallelMap | parallelMap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.0 | NA | R (>= 3.0.0) | BBmisc (>= 1.8), checkmate (>= 1.8.0), parallel, stats, utils | NA | BatchJobs (>= 1.8), batchtools (>= 0.9.6), data.table, Rmpi, rpart, snow, testthat | NA | BSD_2_clause + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| parsedate | parsedate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.0 | NA | NA | rematch2 | NA | covr, testthat, withr | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| party | party | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-4 | NA | R (>= 3.0.0), methods, grid, stats, mvtnorm (>= 1.0-2), modeltools (>= 0.2-21), strucchange | survival (>= 2.37-7), coin (>= 1.1-0), zoo, sandwich (>= 1.1-1) | mvtnorm | TH.data (>= 1.0-3), mlbench, colorspace, MASS, vcd, ipred, varImp | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| partykit | partykit | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2-7 | NA | R (>= 3.1.0), graphics, grid, libcoin (>= 1.0-0), mvtnorm | grDevices, stats, utils, survival, Formula (>= 1.2-1), inum (>= 1.0-0), rpart (>= 4.1-11) | NA | XML, pmml, rJava, sandwich, strucchange, vcd, AER, mlbench, TH.data (>= 1.0-3), coin (>= 1.1-0), RWeka (>= 0.4-19), datasets, parallel, psychotools (>= 0.3-0), psychotree, party (>= 1.3-0) | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| pastecs | pastecs | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.21 | NA | NA | boot, stats, graphics, utils, grDevices | NA | svUnit, covr | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| pathview | pathview | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.24.0 | NA | R (>= 2.10), org.Hs.eg.db | KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils | NA | gage, org.Mm.eg.db, RUnit, BiocGenerics | NA | GPL (>=3.0) | NA | NA | NA | NA | no | 3.6.1 |
| pbapply | pbapply | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-2 | NA | R (>= 3.2.0) | parallel | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| pbivnorm | pbivnorm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.0 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| pbkrtest | pbkrtest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-8.6 | NA | R (>= 3.6.0), lme4 (>= 1.1.10) | Matrix (>= 1.2.3), parallel, magrittr, MASS, methods | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| pca3d | pca3d | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.10.1 | NA | R (>= 2.10) | rgl,ellipse | NA | knitr | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| pec | pec | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2019.11.03 | NA | R (>= 2.9.0), prodlim (>= 1.4.9) | foreach (>= 1.4.2), rms (>= 4.2-0), survival (>= 2.37-7), timereg (>= 1.8.9) | NA | randomForestSRC, party, cmprsk (>= 2.2-7), rpart, CoxBoost, crrstep, riskRegression (>= 1.0.8), lava (>= 1.4.1), Hmisc (>= 3.14-4) | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| permute | permute | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-5 | NA | R (>= 2.14.0) | stats | NA | vegan (>= 2.0-0), testthat (>= 0.5), parallel | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| pheatmap | pheatmap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.12 | NA | R (>= 2.0) | grid, RColorBrewer, scales, gtable, stats, grDevices, graphics | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| pillar | pillar | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.4 | NA | NA | cli, crayon (>= 1.3.4), fansi, rlang (>= 0.3.0), utf8 (>= 1.1.0), vctrs (>= 0.2.0) | NA | knitr, lubridate, testthat (>= 2.0.0), withr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| pingr | pingr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.0 | NA | NA | processx, utils | NA | covr, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| pinp | pinp | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0.9 | NA | NA | rmarkdown, knitr | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| pixmap | pixmap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-11 | NA | methods | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | NA | 3.6.2 |
| pkgbuild | pkgbuild | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.8 | NA | R (>= 3.1) | callr (>= 3.2.0), cli, crayon, desc, prettyunits, R6, rprojroot, withr (>= 2.1.2) | NA | Rcpp, testthat, covr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| pkgconfig | pkgconfig | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.3 | NA | NA | utils | NA | covr, testthat, disposables (>= 1.0.3) | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| pkgdown | pkgdown | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5.1 | NA | R (>= 3.1.0) | callr (>= 2.0.2), cli, crayon, desc, digest, evaluate, fs (>= 1.3.0), fansi, highlight, httr, magrittr, MASS, memoise, openssl, purrr, processx, rematch2, rlang (>= 0.3.0), rmarkdown (>= 1.1.9007), rstudioapi, tibble, tools, whisker, withr, xml2 (>= 1.3.1), yaml | NA | covr, htmlwidgets, jsonlite, knitr, leaflet, pkgload (>= 1.0.2), testthat (>= 2.1.0), rticles, rsconnect | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| pkgload | pkgload | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.2 | NA | NA | desc, methods, pkgbuild, rlang, rprojroot, rstudioapi, utils, withr | NA | bitops, covr, Rcpp, testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| plogr | plogr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.0 | NA | NA | NA | NA | Rcpp | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| plotly | plotly | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.9.2.1 | NA | R (>= 3.2.0), ggplot2 (>= 3.0.0) | tools, scales, httr, jsonlite (>= 1.6), magrittr, digest, viridisLite, base64enc, htmltools (>= 0.3.6), htmlwidgets (>= 1.3), tidyr, hexbin, RColorBrewer, dplyr, tibble, lazyeval (>= 0.2.0), rlang, crosstalk, purrr, data.table, promises | NA | MASS, maps, ggthemes, GGally, testthat, knitr, devtools, shiny (>= 1.1.0), shinytest (>= 1.3.0), curl, rmarkdown, vdiffr, Cairo, broom, webshot, listviewer, dendextend, sf, maptools, rgeos, png, IRdisplay, processx, plotlyGeoAssets, forcats | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| plotmo | plotmo | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.5.7 | NA | R (>= 3.4.0), Formula (>= 1.2-3), plotrix, TeachingDemos | NA | NA | C50 (>= 0.1.0-24), earth (>= 5.1.0), gbm (>= 2.1.1), glmnet (>= 2.0.5), glmnetUtils (>= 1.0.3), MASS (>= 7.3-45), mlr (>= 2.12.1), neuralnet (>= 1.33), partykit (>= 1.2-2), pre (>= 0.5.0), rpart (>= 4.1-10), rpart.plot (>= 2.1.0) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| plotrix | plotrix | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.7-8 | NA | R (>= 3.5.0) | grDevices, graphics, stats, utils | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| pls | pls | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.7-2 | NA | R (>= 2.10) | grDevices, graphics, methods, stats | NA | MASS, parallel, Rmpi, testthat, RUnit | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| plyr | plyr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8.6 | NA | R (>= 3.1.0) | Rcpp (>= 0.11.0) | Rcpp | abind, covr, doParallel, foreach, iterators, itertools, tcltk, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| pmml | pmml | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3.1 | NA | XML | methods, stats, utils, stringr | NA | ada, amap, arules, caret, clue, data.table, forecast, gbm, glmnet, Matrix, neighbr, nnet, rpart, randomForestSRC (<= 2.5.0), randomForest, rattle, kernlab, e1071, testthat, survival, xgboost, knitr, rmarkdown, covr | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| png | png | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-7 | NA | R (>= 2.9.0) | NA | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| polspline | polspline | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.18 | NA | NA | stats, graphics | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| polyclip | polyclip | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.10-0 | NA | R (>= 3.0.0) | NA | NA | NA | NA | BSL | NA | NA | NA | NA | yes | 3.6.1 |
| polycor | polycor | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7-10 | NA | R (>= 3.3.0) | stats, mvtnorm, Matrix | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| polynom | polynom | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-0 | NA | NA | stats, graphics | NA | knitr, rmarkdown | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| prabclus | prabclus | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3-2 | NA | R (>= 2.10), MASS, mclust | NA | NA | spdep, spatialreg, bootstrap, maptools, foreign, mvtnorm | NA | GPL | NA | NA | NA | NA | no | 3.6.1 |
| praise | praise | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | NA | NA | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| prediction | prediction | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.14 | NA | R (>= 3.5.0) | utils, stats, data.table | NA | datasets, methods, testthat | AER, aod, betareg, biglm, brglm, caret, crch, e1071, earth, ff, ffbase, gam (>= 1.15), gee, glmnet, glmx, kernlab, lme4, MASS, mclogit, mda, mlogit, MNP, nlme, nnet, ordinal, plm, pscl, quantreg, rpart, sampleSelection, speedglm, survey (>= 3.31-5), survival, truncreg, VGAM | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| preprocessCore | preprocessCore | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.46.0 | NA | NA | stats | NA | NA | NA | LGPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| prettyunits | prettyunits | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.1 | NA | NA | NA | NA | codetools, covr, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| processx | processx | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.4.2 | NA | NA | ps (>= 1.2.0), R6, utils | NA | callr (>= 3.2.0), codetools, covr, crayon, curl, debugme, parallel, testthat, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| prodlim | prodlim | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2019.11.13 | NA | R (>= 2.9.0) | Rcpp (>= 0.11.5), stats, grDevices, graphics, survival, KernSmooth, lava | Rcpp | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| profdpm | profdpm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.3 | NA | NA | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| profileModel | profileModel | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.0 | NA | R (>= 2.6.0) | NA | NA | MASS, gnm | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| profileR | profileR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3-5 | NA | ggplot2, RColorBrewer, reshape, lavaan, R (>= 3.0.0) | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| profmem | profmem | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.0 | NA | NA | utils | NA | R.rsp, markdown, microbenchmark | NA | LGPL (>= 2.1) | NA | NA | NA | NA | no | 3.6.1 |
| profvis | profvis | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.6 | NA | R (>= 3.0) | htmlwidgets (>= 0.3.2), stringr | NA | knitr, ggplot2, rmarkdown, testthat, devtools, shiny, htmltools | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| progress | progress | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.2 | NA | NA | hms, prettyunits, R6, crayon | NA | Rcpp, testthat, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| promises | promises | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | NA | R6, Rcpp, later, rlang, stats, magrittr | later, Rcpp | testthat, future, knitr, rmarkdown | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| proto | proto | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | NA | NA | NA | testthat, covr | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| proxy | proxy | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-24 | NA | R (>= 3.4.0) | stats, utils | NA | cba | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| ps | ps | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.3 | NA | R (>= 3.1) | utils | NA | callr, covr, curl, pingr, processx (>= 3.1.0), R6, rlang, testthat, tibble | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| pspearman | pspearman | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3-0 | NA | NA | NA | NA | NA | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| psych | psych | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.9.12.31 | NA | NA | mnormt,parallel,stats,graphics,grDevices,methods,lattice,nlme | NA | psychTools, GPArotation, lavaan, sem, lme4,Rcsdp, graph, Rgraphviz | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| purrr | purrr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.4 | NA | R (>= 3.2) | magrittr (>= 1.5), rlang (>= 0.3.1) | NA | covr, crayon, dplyr (>= 0.7.8), knitr, rmarkdown, testthat, tibble, tidyselect | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| pvclust | pvclust | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2-0 | NA | R (>= 2.10.0) | NA | NA | MASS, parallel | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| qap | qap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-1 | NA | NA | NA | NA | testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| qtl | qtl | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.46-2 | NA | R (>= 2.14.0) | parallel, graphics, stats, utils, grDevices | NA | testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| quadprog | quadprog | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5-8 | NA | R (>= 3.1.0) | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| quantmod | quantmod | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.17 | NA | R (>= 3.2.0), xts(>= 0.9-0), zoo, TTR(>= 0.2), methods | curl | NA | DBI,RMySQL,RSQLite,timeSeries,XML,downloader,jsonlite(>= 1.1) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| quantreg | quantreg | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.55 | NA | R (>= 2.6), stats, SparseM | methods, graphics, Matrix, MatrixModels | NA | tripack, akima, MASS, survival, rgl, logspline, nor1mix, Formula, zoo, R.rsp | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| questionr | questionr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7.0 | NA | R (>= 2.10) | shiny (>= 1.0.5), miniUI, rstudioapi, highr, classInt, htmltools, graphics, stats, utils, labelled (>= 2.0.0) | NA | memisc, testthat, roxygen2, dplyr, tidyr, janitor, forcats, knitr | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| qvalue | qvalue | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.16.0 | NA | R(>= 2.10) | splines, ggplot2, grid, reshape2 | NA | knitr | NA | LGPL | NA | NA | NA | NA | no | 3.6.1 |
| qvcalc | qvcalc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.2 | NA | NA | NA | NA | relimp, MASS | psychotools, survival | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| rARPACK | rARPACK | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.11-0 | NA | NA | RSpectra | NA | Matrix (>= 1.1-0) | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| rJava | rJava | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-12 | NA | R (>= 2.5.0), methods | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| randomForest | randomForest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.6-14 | NA | R (>= 3.2.2), stats | NA | NA | RColorBrewer, MASS | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| ranger | ranger | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.12.1 | NA | R (>= 3.1) | Rcpp (>= 0.11.2), Matrix | Rcpp, RcppEigen | survival, testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| rappdirs | rappdirs | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.1 | NA | R (>= 2.14), methods | NA | NA | testthat, roxygen2 | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| raster | raster | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.1-5 | NA | sp (>= 1.2-0), R (>= 3.0.0) | Rcpp, methods | Rcpp | rgdal (>= 0.9-1), rgeos (>= 0.3-8), ncdf4, igraph, tcltk, parallel, rasterVis, MASS, sf, testthat | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.2 |
| rattle | rattle | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.3.0 | NA | R (>= 3.5.0) | stats, utils, ggplot2, grDevices, graphics, magrittr, methods, stringi, stringr, tidyr, dplyr, XML, rpart.plot | NA | pmml (>= 1.2.13), bitops, colorspace, ada, amap, arules, arulesViz, biclust, cairoDevice, cba, cluster, corrplot, descr, doBy, e1071, ellipse, fBasics, foreign, fpc, gdata, ggdendro, ggraptR, gplots, grid, gridExtra, gtools, gWidgetsRGtk2, hmeasure, Hmisc, kernlab, Matrix, mice, nnet, party, plyr, psych, randomForest, RColorBrewer, readxl, reshape, rggobi, RGtk2, ROCR, RODBC, rpart, scales, SnowballC, survival, timeDate, tm, verification, wskm, xgboost | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| rattle.data | rattle.data | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.2 | NA | R (>= 2.10) | NA | NA | rattle | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| rcmdcheck | rcmdcheck | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.3 | NA | NA | callr (>= 3.1.1.9000), cli (>= 1.1.0), crayon, desc (>= 1.2.0), digest, pkgbuild, prettyunits, R6, rprojroot, sessioninfo (>= 1.1.1), utils, withr, xopen | NA | covr, knitr, mockery, rmarkdown, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| readbitmap | readbitmap | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.5 | NA | NA | bmp, jpeg, png, tiff | NA | pixmap, testthat | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| readr | readr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.1 | NA | R (>= 3.1) | Rcpp (>= 0.12.0.5), tibble, hms (>= 0.4.1), R6, clipr, crayon, methods | Rcpp, BH | curl, testthat, knitr, rmarkdown, stringi, covr, spelling | NA | GPL (>= 2) | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| readxl | readxl | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.1 | NA | NA | cellranger, Rcpp (>= 0.12.18), tibble (>= 1.3.1), utils | progress, Rcpp | covr, knitr, rmarkdown, rprojroot (>= 1.1), testthat | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| rebus | rebus | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-3 | NA | R (>= 3.1.0) | rebus.base (>= 0.0-3), rebus.datetimes, rebus.numbers, rebus.unicode (>= 0.0-2) | NA | testthat | NA | Unlimited | NA | NA | NA | NA | no | 3.6.1 |
| rebus.base | rebus.base | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-3 | NA | R (>= 3.1.0) | stats | NA | stringi, testthat | NA | Unlimited | NA | NA | NA | NA | no | 3.6.1 |
| rebus.datetimes | rebus.datetimes | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-1 | NA | R (>= 3.1.0) | rebus.base | NA | stats, testthat | NA | Unlimited | NA | NA | NA | NA | no | 3.6.1 |
| rebus.numbers | rebus.numbers | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-1 | NA | R (>= 3.1.0) | rebus.base, utils | NA | testthat | NA | Unlimited | NA | NA | NA | NA | no | 3.6.1 |
| rebus.unicode | rebus.unicode | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.0-2 | NA | R (>= 3.1.0) | rebus.base (>= 0.0-2) | NA | stringi | NA | Unlimited | NA | NA | NA | NA | no | 3.6.1 |
| recipes | recipes | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.12 | NA | R (>= 3.1), dplyr | generics, glue, gower, ipred, lubridate, magrittr, Matrix, purrr (>= 0.2.3), rlang (>= 0.4.0), stats, tibble, tidyr (>= 0.8.3), tidyselect (>= 0.2.5), timeDate, utils, withr | NA | covr, ddalpha, dimRed (>= 0.2.2), fastICA, ggplot2, igraph, kernlab, knitr, modeldata, pls, RANN, RcppRoll, rmarkdown, rpart, rsample, RSpectra, testthat (>= 2.1.0), xml2 | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| reghelper | reghelper | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.6 | NA | R (>= 3.1.0) | ggplot2 (>= 1.0.0), stats, nlme, lme4, utils | NA | testthat (>= 0.8.1) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| registry | registry | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5-1 | NA | R (>= 2.6.0) | utils | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| regress | regress | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-15 | NA | NA | NA | NA | nlme, MASS | NA | GPL | NA | NA | NA | NA | no | 3.6.1 |
| rematch | rematch | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | NA | NA | NA | covr, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| rematch2 | rematch2 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1.2 | NA | NA | tibble | NA | covr, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| remote | remote | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.1 | NA | R (>= 2.10), Rcpp (>= 0.10.3), raster, methods | grDevices, gridExtra, latticeExtra, mapdata, scales, stats, utils | Rcpp | maps, lattice, grid, sp | NA | GPL (>= 3) | file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| remotes | remotes | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1.1 | NA | R (>= 3.0.0) | methods, stats, tools, utils | NA | brew, callr, codetools, curl, covr, git2r (>= 0.23.0), knitr, mockery, pkgbuild (>= 1.0.1), pingr, rmarkdown, rprojroot, testthat, withr | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| repr | repr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | R (>= 3.0.1) | utils, grDevices, htmltools, jsonlite, pillar (>= 1.4.0), base64enc | NA | methods, highr, Cairo, stringr, testthat, diffobj (>= 0.2.3), leaflet | data.table, dplyr, htmlwidgets, vegalite, plotly, geojsonio | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| reprex | reprex | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 3.1) | callr (>= 2.0.0), clipr (>= 0.4.0), fs, rlang, rmarkdown, utils, whisker, withr | NA | covr, devtools, fortunes, knitr, miniUI, rprojroot, rstudioapi, shiny, styler (>= 1.0.2), testthat (>= 2.0.0) | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| repurrrsive | repurrrsive | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | R (>= 2.10) | tibble, utils | NA | gapminder, jsonlite, purrr, rprojroot, testthat (>= 2.1.0), wesanderson, xml2 | NA | CC0 | NA | NA | NA | NA | no | 3.6.1 |
| reshape | reshape | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.8.8 | NA | R (>= 2.6.1) | plyr | NA | NA | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| reshape2 | reshape2 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.4 | NA | R (>= 3.1) | plyr (>= 1.8.1), Rcpp, stringr | Rcpp | covr, lattice, testthat (>= 0.8.0) | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| reticulate | reticulate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.15 | NA | R (>= 3.0) | graphics, jsonlite, Matrix, methods, rappdirs, Rcpp (>= 0.12.7), utils | Rcpp | callr, knitr, rmarkdown, testthat | NA | Apache License 2.0 | NA | NA | NA | NA | yes | 3.6.2 |
| rex | rex | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.0 | NA | NA | lazyeval | NA | testthat, knitr, rmarkdown, dplyr, ggplot2, magrittr, Hmisc, stringr, rvest, roxygen2, covr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| rgeos | rgeos | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5-3 | NA | R (>= 3.3.0), methods, sp (>= 1.1-0) | utils, stats, graphics | sp | maptools (>= 0.8-5), testthat, XML, maps, rgdal | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| rgexf | rgexf | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.16.0 | NA | NA | XML, igraph, grDevices, utils, servr | NA | knitr, rmarkdown, testthat, covr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| rgl | rgl | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.100.54 | NA | R (>= 3.2.0) | graphics, grDevices, stats, utils, htmlwidgets, htmltools, knitr, jsonlite (>= 0.9.20), shiny, magrittr, crosstalk, manipulateWidget (>= 0.9.0) | NA | MASS, rmarkdown, deldir, orientlib, lattice, misc3d, rstudioapi, magick, plotrix (>= 3.7-3), tripack, interp, alphashape3d, tcltk | NA | GPL | NA | NA | NA | NA | yes | 3.6.2 |
| rhdf5 | rhdf5 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.28.1 | NA | R (>= 3.5.0), methods | Rhdf5lib (>= 1.3.2) | Rhdf5lib | bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark, dplyr, ggplot2 | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| rhub | rhub | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.1 | NA | NA | assertthat, callr, cli (>= 1.1.0), crayon, desc, digest, httr, jsonlite, parsedate, pillar, prettyunits, processx, R6, rappdirs, rcmdcheck (>= 1.2.1), rematch, tibble, utils, uuid, whoami, withr | NA | covr, testthat, knitr, rmarkdown | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| rio | rio | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.16 | NA | R (>= 2.15.0) | tools, stats, utils, foreign, haven (>= 1.1.0), curl (>= 0.6), data.table (>= 1.9.8), readxl (>= 0.1.1), openxlsx, tibble | NA | datasets, bit64, testthat, knitr, magrittr, clipr, csvy, feather, fst, hexView, jsonlite, readODS (>= 1.6.4), readr, rmatio, xml2 (>= 1.2.0), yaml | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| rjson | rjson | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.20 | NA | R (>= 3.1.0) | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| rlang | rlang | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.6 | NA | R (>= 3.2.0) | NA | NA | cli, covr, crayon, glue, magrittr, methods, pillar, rmarkdown, testthat (>= 2.3.0), vctrs (>= 0.2.3) | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| rmarkdown | rmarkdown | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1 | NA | R (>= 3.0) | tools, utils, knitr (>= 1.22), yaml (>= 2.1.19), htmltools (>= 0.3.5), evaluate (>= 0.13), base64enc, jsonlite, mime, tinytex (>= 0.11), xfun, methods, stringr (>= 1.2.0) | NA | shiny (>= 0.11), tufte, testthat, digest, dygraphs, tibble, fs, pkgdown, callr (>= 2.0.0) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| rmdformats | rmdformats | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.7 | NA | NA | knitr, rmarkdown, bookdown, htmltools | NA | questionr | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| rmeta | rmeta | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0 | NA | NA | grid, stats, graphics | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| rms | rms | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.1-4 | NA | R (>= 3.5.0), Hmisc (>= 4.3-0), survival (>= 3.1-6), lattice, ggplot2 (>= 2.2), SparseM | methods, quantreg, rpart, nlme (>= 3.1-123), polspline, multcomp, htmlTable (>= 1.11.0), htmltools | NA | boot, tcltk, plotly (>= 4.5.6) | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| rngtools | rngtools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5 | NA | R (>= 3.2.0), methods | digest, utils, stats, parallel | NA | covr, RUnit, testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| robustbase | robustbase | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.93-6 | NA | R (>= 3.1.0) | stats, graphics, utils, methods, DEoptimR | NA | grid, MASS, lattice, boot, cluster, Matrix, robust, fit.models, MPV, xtable, ggplot2, GGally, RColorBrewer, reshape2, sfsmisc, catdata, doParallel, foreach, skewt | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| rowr | rowr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.3 | NA | R (>= 3.0.1) | methods | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| roxygen2 | roxygen2 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 7.1.0 | NA | R (>= 3.2) | brew, commonmark, desc (>= 1.2.0), digest, knitr, methods, pkgload (>= 1.0.2), purrr (>= 0.3.3), R6 (>= 2.1.2), Rcpp (>= 0.11.0), rlang, stringi, stringr (>= 1.0.0), utils, xml2 | Rcpp | covr, devtools, rmarkdown, testthat (>= 2.1.0), R.methodsS3, R.oo | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| roxygen2md | roxygen2md | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | NA | desc, devtools, enc, rex, rlang, tibble, usethis, withr | NA | rstudioapi, testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| rpart | rpart | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 4.1-15 | recommended | R (>= 2.15.0), graphics, stats, grDevices | NA | NA | survival | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| rpart.plot | rpart.plot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0.8 | NA | R (>= 3.4.0), rpart (>= 4.1-10) | NA | NA | earth (>= 5.1.0) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| rpartScore | rpartScore | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-1 | NA | R (>= 2.14.2), rpart | NA | NA | MASS | NA | GPL (>= 2) | NA | NA | NA | NA | NA | 3.6.0 |
| rprojroot | rprojroot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3-2 | NA | R (>= 3.0.0) | backports | NA | testthat, mockr, knitr, withr, rmarkdown | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| rsnps | rsnps | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | NA | plyr, stringr, crul (>= 0.5.2), data.table, XML, xml2, jsonlite | NA | testthat, knitr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| rsq | rsq | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0 | NA | NA | methods, stats, MASS, lme4, nlme, numDeriv, Matrix | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 | |
| rstatix | rstatix | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.0 | NA | R (>= 3.3.0) | stats, utils, tidyr (>= 1.0.0), purrr, broom, rlang (>= 0.3.1), tibble (>= 2.1.3), dplyr (>= 0.7.1), magrittr, corrplot, tidyselect (>= 1.0.0), car | NA | knitr, rmarkdown, ggpubr, graphics, emmeans, coin, boot, testthat, spelling | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| rstudioapi | rstudioapi | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.11 | NA | NA | NA | NA | testthat, knitr, rmarkdown, clipr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| rsvd | rsvd | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.3 | NA | R (>= 3.2.2) | Matrix | NA | ggplot2, testthat | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.2 |
| rtracklayer | rtracklayer | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.44.4 | NA | R (>= 3.3), methods, GenomicRanges (>= 1.31.8) | XML (>= 1.98-0), BiocGenerics (>= 0.25.1), S4Vectors (>= 0.19.22), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), tools | S4Vectors, IRanges, XVector | BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit | NA | Artistic-2.0 + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| rvcheck | rvcheck | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.8 | NA | R (>= 3.4.0) | BiocManager, utils, rlang | NA | NA | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.2 |
| rversions | rversions | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.1 | NA | NA | curl, utils, xml2 (>= 1.0.0) | NA | mockery, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| rvest | rvest | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.5 | NA | R (>= 3.2), xml2 | httr (>= 0.5), magrittr, selectr | NA | covr, knitr, png, rmarkdown, spelling, stringi (>= 0.3.1), testthat | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| sandwich | sandwich | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.5-1 | NA | R (>= 2.10.0) | stats, utils, zoo | NA | AER, car, geepack, lattice, lmtest, MASS, multiwayvcov, parallel, pcse, plm, pscl, scatterplot3d, stats4, strucchange, survival | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| scales | scales | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.1 | NA | R (>= 3.2) | farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6, RColorBrewer, viridisLite | NA | bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), testthat (>= 2.1.0) | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| scater | scater | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.12.2 | NA | R (>= 3.6), SingleCellExperiment, ggplot2 | BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel | Rcpp, beachmat | BiocStyle, biomaRt, beachmat, cowplot, destiny, knitr, mvoutlier, rmarkdown, Rtsne, uwot, testthat, magrittr, pheatmap, Biobase, limma | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.0 |
| scatterplot3d | scatterplot3d | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3-41 | NA | R (>= 2.7.0) | grDevices, graphics, stats | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| segmented | segmented | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-0 | NA | NA | NA | NA | NA | NA | GPL | NA | NA | NA | NA | no | 3.6.1 |
| selectr | selectr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-2 | NA | R (>= 3.0) | methods, stringr, R6 | NA | testthat, XML, xml2 | NA | BSD_3_clause + file LICENCE | NA | NA | NA | NA | no | 3.6.1 |
| seqinr | seqinr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.6-1 | NA | R (>= 2.10.0) | ade4,segmented | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| seriation | seriation | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2-8 | NA | R (>= 2.14.0) | TSP, qap, grid, cluster, gclus, dendextend, colorspace, MASS, gplots, registry, methods, stats, grDevices | NA | biclust, testthat, DendSer, GA | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| servr | servr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.16 | NA | R (>= 3.0.0) | mime (>= 0.2), httpuv (>= 1.4.0), xfun, jsonlite | NA | tools, later, rstudioapi, knitr (>= 1.9), rmarkdown | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| sessioninfo | sessioninfo | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.1 | NA | NA | cli, tools, utils, withr | NA | callr, covr, mockery, testthat | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| sf | sf | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9-3 | NA | methods, R (>= 3.3.0) | classInt (>= 0.4-1), DBI (>= 0.8), graphics, grDevices, grid, magrittr, Rcpp (>= 0.12.18), stats, tools, units (>= 0.6-0), utils | Rcpp | blob, covr, dplyr (>= 0.8-3), ggplot2, knitr, lwgeom (>= 0.2-1), maps, mapview, microbenchmark, odbc, pillar, pool, raster, rgdal, rgeos, rlang, rmarkdown, RPostgres (>= 1.1.0), RPostgreSQL, RSQLite, sp (>= 1.2-4), spatstat, spatstat.utils, stars (>= 0.2-0), testthat, tibble (>= 1.4.1), tidyr (>= 1.0-0), tmap (>= 2.0), vctrs | NA | GPL-2 | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| shape | shape | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.4 | NA | R (>= 2.01) | stats, graphics, grDevices | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | no | 3.6.1 |
| shiny | shiny | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.0.2 | NA | R (>= 3.0.2), methods | utils, grDevices, httpuv (>= 1.5.2), mime (>= 0.3), jsonlite (>= 0.9.16), xtable, digest, htmltools (>= 0.4.0), R6 (>= 2.0), sourcetools, later (>= 1.0.0), promises (>= 1.1.0), tools, crayon, rlang (>= 0.4.0), fastmap (>= 1.0.0) | NA | datasets, Cairo (>= 1.5-5), testthat (>= 2.1.1), knitr (>= 1.6), markdown, rmarkdown, ggplot2, reactlog (>= 1.0.0), magrittr, yaml | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| shinythemes | shinythemes | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.2 | NA | R (>= 3.0.0) | shiny (>= 0.11) | NA | NA | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| slam | slam | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-47 | NA | R (>= 3.4.0) | stats | NA | NA | Matrix, SparseM, spam | GPL-2 | NA | NA | NA | NA | yes | 3.6.1 |
| snakecase | snakecase | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.11.0 | NA | R (>= 3.2) | stringr, stringi | NA | testthat, covr, tibble, purrrlyr, knitr, rmarkdown, magrittr | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| snow | snow | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-3 | NA | R (>= 2.13.1), utils | NA | NA | Rmpi,rlecuyer,nws | NA | GPL | NA | NA | NA | NA | no | 3.6.2 |
| snpStats | snpStats | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.34.0 | NA | R(>= 2.10.0), survival, Matrix, methods | graphics, grDevices, stats, utils, BiocGenerics, zlibbioc | NA | hexbin | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| sourcetools | sourcetools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.7 | NA | R (>= 3.0.2) | NA | NA | testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| sp | sp | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-1 | NA | R (>= 3.0.0), methods | utils, stats, graphics, grDevices, lattice, grid | NA | RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat, maptools, deldir | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| spFSR | spFSR | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | mlr (>= 2.11), parallelMap (>= 1.3), parallel (>= 3.4.2), tictoc (>= 1.0) | ggplot2 (>= 2.2.1), class (>= 7.3), mlbench (>= 2.1) | NA | caret (>= 6.0), MASS (>= 7.3), knitr, rmarkdown | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| spam | spam | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.5-1 | NA | R (>= 3.1), dotCall64, grid, methods | NA | NA | spam64, fields, SparseM, Matrix, testthat, R.rsp, truncdist, knitr, rmarkdown | NA | LGPL-2 | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| spelling | spelling | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.1 | NA | NA | commonmark, xml2, hunspell (>= 3.0), knitr | NA | pdftools | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| spls | spls | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2-3 | NA | R (>= 2.14) | MASS, nnet, parallel, pls | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| sqldf | sqldf | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4-11 | NA | R (>= 3.1.0), gsubfn (>= 0.6), proto, RSQLite | DBI, chron | NA | RH2, RMySQL, RPostgreSQL, svUnit, tcltk, MASS | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| stabledist | stabledist | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7-1 | NA | R (>= 3.1.0) | stats | NA | Matrix, fBasics, FMStable, RUnit, Rmpfr, sfsmisc | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| stabs | stabs | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6-3 | NA | R (>= 2.14.0), methods, stats, parallel | graphics, grDevices, utils | NA | glmnet, lars, mboost (> 2.3-0), gamboostLSS (>= 1.2-0), QUIC, TH.data, hdi, testthat, knitr, rmarkdown, igraph, huge | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| stargazer | stargazer | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 5.2.2 | NA | NA | stats, utils | NA | NA | AER, betareg, brglm, censReg, dynlm, eha, erer, ergm, fGarch, gee, glmx, gmm, lfe, lme4, lmtest, MASS, mclogit, mgcv, mlogit, mnlogit, nlme, nnet, ordinal, plm, pscl, quantreg, rms, relevent, robustbase, sampleSelection, spdep, survey, survival, Zelig | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| statmod | statmod | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.34 | NA | R (>= 3.0.0) | stats, graphics | NA | MASS, tweedie | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| stepPlr | stepPlr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.93 | NA | R (>= 2.0) | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| stringdist | stringdist | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.9.5.5 | NA | R (>= 2.15.3) | parallel | NA | tinytest | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| stringi | stringi | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.6 | NA | R (>= 2.14) | tools, utils, stats | NA | NA | NA | file LICENSE | yes | NA | NA | NA | yes | 3.6.2 |
| stringr | stringr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.0 | NA | R (>= 3.1) | glue (>= 1.2.0), magrittr, stringi (>= 1.1.7) | NA | covr, htmltools, htmlwidgets, knitr, rmarkdown, testthat | NA | GPL-2 | file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| strucchange | strucchange | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.5-2 | NA | R (>= 2.10.0), zoo, sandwich | graphics, stats, utils | NA | stats4, car, dynlm, e1071, foreach, lmtest, mvtnorm, tseries | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| subselect | subselect | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.15.2 | NA | R (>= 3.5.0) | MASS, ISwR, corpcor | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| superpc | superpc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.09 | NA | survival | NA | NA | NA | NA | GPL-2 | NA | NA | NA | NA | NA | 3.6.1 |
| survAUC | survAUC | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-5 | NA | R (>= 2.6.0), survival | NA | NA | rms | NA | GPL-2 | NA | NA | NA | NA | NA | 3.6.0 |
| survMisc | survMisc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.5 | NA | survival | graphics, grDevices, stats, utils, knitr, KMsurv, ggplot2, data.table, zoo, grid, gridExtra, km.ci, xtable | NA | NA | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.0 |
| survcomp | survcomp | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.34.0 | NA | survival, prodlim, R (>= 3.4) | ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics | NA | Hmisc, CPE, clinfun, xtable, Biobase, BiocManager | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.0 |
| survival | survival | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.1-12 | recommended | R (>= 3.4.0) | graphics, Matrix, methods, splines, stats, utils | NA | NA | NA | LGPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| survivalROC | survivalROC | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.3 | NA | R (>= 1.6.1) | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | NA | 3.6.0 |
| survminer | survminer | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.6 | NA | ggplot2, ggpubr(>= 0.1.6) | grid, gridExtra (>= 2.0), magrittr, maxstat, methods, scales, survival, stats, broom, dplyr, tidyr, survMisc, purrr, tibble | NA | knitr, flexsurv, cmprsk | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| sva | sva | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.32.1 | NA | R (>= 3.2), mgcv, genefilter, BiocParallel | matrixStats, stats, graphics, utils, limma, | NA | pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| svglite | svglite | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.3 | NA | R (>= 3.0.0) | Rcpp, gdtools (>= 0.1.6) | Rcpp, gdtools, BH | htmltools, testthat, xml2 (>= 1.0.0), covr, fontquiver (>= 0.2.0), knitr, rmarkdown | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| swirl | swirl | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.4.5 | NA | R (>= 3.1.0) | stringr, testthat (>= 1.0.2), httr (>= 1.1.0), yaml, RCurl, digest, tools, methods | NA | stringi | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| synbreed | synbreed | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.12-9 | NA | R (>= 2.14) | abind, BGLR, doBy, doParallel, foreach, igraph, lattice, qtl, regress (>= 1.3-8), MASS, methods, LDheatmap | NA | synbreedData (>= 1.5) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| sys | sys | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.3 | NA | NA | NA | NA | unix (>= 1.4), spelling, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| systemfonts | systemfonts | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.2.2 | NA | NA | NA | NA | testthat (>= 2.1.0), covr, knitr, rmarkdown, tools | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| tensorflow | tensorflow | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2.0 | NA | R (>= 3.1) | config, jsonlite (>= 1.2), processx, reticulate (>= 1.10), tfruns (>= 1.0), utils, yaml, rstudioapi (>= 0.7) | NA | testthat (>= 2.1.0), keras, tfestimators, callr | NA | Apache License 2.0 | NA | NA | NA | NA | no | 3.6.2 |
| testthat | testthat | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.3.2 | NA | R (>= 3.1) | cli, crayon (>= 1.3.4), digest, ellipsis, evaluate, magrittr, methods, pkgload, praise, R6 (>= 2.2.0), rlang (>= 0.4.1), withr (>= 2.0.0) | NA | covr, curl (>= 0.9.5), devtools, knitr, rmarkdown, usethis, vctrs (>= 0.1.0), xml2 | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| tfruns | tfruns | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4 | NA | R (>= 3.1) | utils, jsonlite (>= 1.2), base64enc, yaml, config, magrittr, whisker, tidyselect, rlang, rstudioapi (>= 0.7), reticulate | NA | testthat, knitr | NA | Apache License 2.0 | NA | NA | NA | NA | no | 3.6.1 |
| tibble | tibble | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.0.1 | NA | R (>= 3.1.0) | cli, crayon (>= 1.3.4), ellipsis (>= 0.2.0), fansi (>= 0.4.0), lifecycle (>= 0.2.0), magrittr, methods, pillar (>= 1.4.3), pkgconfig, rlang (>= 0.4.3), utils, vctrs (>= 0.2.4) | NA | bench, bit64, blob, covr, dplyr, evaluate, hms, htmltools, import, knitr, mockr, nycflights13, purrr, rmarkdown, testthat (>= 2.1.0), tidyr, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| tictoc | tictoc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0 | NA | R (>= 3.0.3), methods | NA | NA | NA | NA | Apache License (== 2.0) | file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| tidygraph | tidygraph | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.2.0 | NA | NA | tibble, dplyr (>= 0.8.5), igraph, magrittr, utils, rlang, R6, Rcpp, tools, stats, tidyr, pillar | Rcpp | network, data.tree, ape, graph, methods, testthat, covr, seriation, netrankr, influenceR, NetSwan | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| tidyr | tidyr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.3 | NA | R (>= 3.1) | dplyr (>= 0.8.2), ellipsis (>= 0.1.0), glue, magrittr, purrr, Rcpp, rlang, stringi, tibble (>= 2.1.1), tidyselect (>= 0.2.5), utils, vctrs (>= 0.2.0), lifecycle | Rcpp | covr, jsonlite, knitr, repurrrsive (>= 1.0.0), rmarkdown, readr, testthat (>= 2.1.0) | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| tidyselect | tidyselect | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.0 | NA | R (>= 3.2) | ellipsis, glue (>= 1.3.0), purrr (>= 0.3.2), rlang (>= 0.4.6), vctrs (>= 0.2.2) | NA | covr, crayon, dplyr, knitr, magrittr, rmarkdown, testthat (>= 2.3.0), tibble (>= 2.1.3), withr | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| tidyverse | tidyverse | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.0 | NA | R (>= 3.2) | broom (>= 0.5.2), cli (>= 1.1.0), crayon (>= 1.3.4), dbplyr (>= 1.4.2), dplyr (>= 0.8.3), forcats (>= 0.4.0), ggplot2 (>= 3.2.1), haven (>= 2.2.0), hms (>= 0.5.2), httr (>= 1.4.1), jsonlite (>= 1.6), lubridate (>= 1.7.4), magrittr (>= 1.5), modelr (>= 0.1.5), pillar (>= 1.4.2), purrr (>= 0.3.3), readr (>= 1.3.1), readxl (>= 1.3.1), reprex (>= 0.3.0), rlang (>= 0.4.1), rstudioapi (>= 0.10), rvest (>= 0.3.5), stringr (>= 1.4.0), tibble (>= 2.1.3), tidyr (>= 1.0.0), xml2 (>= 1.2.2) | NA | covr, feather, glue, knitr, rmarkdown, testthat | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| tiff | tiff | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-5 | NA | R (>= 2.9.0) | NA | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| timeDate | timeDate | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3043.102 | NA | R (>= 2.15.1), graphics, utils, stats, methods | NA | NA | date, RUnit | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| timeSeries | timeSeries | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3062.100 | NA | R (>= 2.10), graphics, grDevices, stats, methods, utils, timeDate (>= 2150.95) | NA | NA | RUnit, robustbase, xts, PerformanceAnalytics, fTrading | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| timereg | timereg | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.9.4 | NA | R (>= 2.15), survival | lava, numDeriv, stats, graphics, grDevices, utils, methods | NA | mets, | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| tinytex | tinytex | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.22 | NA | NA | xfun (>= 0.5) | NA | testit, rstudioapi | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| tm | tm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7-7 | NA | R (>= 3.2.0), NLP (>= 0.2-0) | Rcpp, parallel, slam (>= 0.1-37), stats, tools, utils, graphics, xml2 | BH, Rcpp | antiword, filehash, methods, pdftools, Rcampdf, Rgraphviz, Rpoppler, SnowballC, testthat, tm.lexicon.GeneralInquirer | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| triebeard | triebeard | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | NA | Rcpp | Rcpp | knitr, rmarkdown, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| truncnorm | truncnorm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0-8 | NA | R (>= 3.4.0) | NA | NA | testthat | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| tweeDEseq | tweeDEseq | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.30.0 | NA | R (>= 2.12.0) | MASS, limma, edgeR, parallel, cqn | NA | tweeDEseqCountData, xtable | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| tweenr | tweenr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | R (>= 3.2.0) | Rcpp (>= 0.12.3), grDevices, farver, magrittr, rlang | Rcpp | testthat, covr | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| ucminf | ucminf | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1-4 | NA | NA | NA | NA | numDeriv | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.0 |
| units | units | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6-6 | NA | R (>= 3.0.2) | Rcpp | Rcpp (>= 0.12.10) | udunits2, NISTunits, measurements, xml2, tibble, pillar (>= 1.3.0), knitr, testthat, ggforce, rmarkdown, magrittr | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| urltools | urltools | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.7.3 | NA | R (>= 2.10) | Rcpp, methods, triebeard | Rcpp | testthat, knitr | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| usethis | usethis | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.6.1 | NA | R (>= 3.2) | clipr (>= 0.3.0), cli, crayon, curl (>= 2.7), desc, fs (>= 1.3.0), gh (>= 1.1.0), git2r (>= 0.23), glue (>= 1.3.0), purrr, rematch2, rlang (>= 0.4.3), rprojroot (>= 1.2), rstudioapi, stats, utils, whisker, withr, yaml | NA | covr, knitr, magick, pkgdown (>= 1.4.0), rmarkdown, roxygen2, spelling (>= 1.2), styler (>= 1.2.0), testthat (>= 2.1.0) | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| utf8 | utf8 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.1.4 | NA | R (>= 2.10) | NA | NA | knitr, rmarkdown, testthat | NA | Apache License (== 2.0) | file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| uuid | uuid | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1-4 | NA | R (>= 2.9.0) | NA | NA | NA | NA | MIT + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| varSelRF | varSelRF | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.7-8 | NA | R (>= 2.0.0), randomForest, parallel | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| vcd | vcd | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4-7 | NA | R (>= 2.4.0), grid | stats, utils, MASS, grDevices, colorspace, lmtest | NA | KernSmooth, mvtnorm, kernlab, HSAUR, coin | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.2 |
| vctrs | vctrs | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 3.2) | ellipsis (>= 0.2.0), digest, glue, rlang (>= 0.4.5) | NA | bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr, pillar (>= 1.4.4), pkgdown, rmarkdown, testthat (>= 2.3.0), tibble, withr, xml2, zeallot | NA | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| vdiffr | vdiffr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.1 | NA | R (>= 3.2.0) | devtools, diffobj, fontquiver (>= 0.2.0), freetypeharfbuzz (>= 0.2.5), gdtools, glue, grDevices, htmlwidgets (>= 0.6), htmltools, purrr (>= 0.2.0), rlang, R6, Rcpp, shiny, testthat (>= 1.0.0), usethis (>= 1.4.0), xml2 (>= 1.0.0) | freetypeharfbuzz, gdtools, Rcpp, BH | crayon, ggplot2 (>= 3.2.0), roxygen2, rstudioapi, withr, yaml | NA | GPL-3 | file LICENSE | NA | NA | NA | NA | yes | 3.6.1 |
| vegan | vegan | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.5-6 | NA | permute (>= 0.9-0), lattice, R (>= 3.4.0) | MASS, cluster, mgcv | NA | parallel, tcltk, knitr | NA | GPL-2 | NA | NA | NA | NA | yes | 3.6.2 |
| verification | verification | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.42 | NA | R (>= 2.10), methods, fields, boot, CircStats, MASS, dtw | graphics, stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.1 |
| vipor | vipor | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4.5 | NA | R (>= 3.0.0) | stats, graphics | NA | testthat, beeswarm, lattice, ggplot2, beanplot, vioplot, ggbeeswarm, | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| viridis | viridis | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.1 | NA | R (>= 2.10), viridisLite (>= 0.3.0) | stats, ggplot2 (>= 1.0.1), gridExtra | NA | hexbin (>= 1.27.0), scales, MASS, knitr, dichromat, colorspace, rasterVis, httr, mapproj, vdiffr, svglite (>= 1.2.0), testthat, covr, rmarkdown, rgdal | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| viridisLite | viridisLite | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.3.0 | NA | R (>= 2.10) | NA | NA | hexbin (>= 1.27.0), ggplot2 (>= 1.0.1), testthat, covr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| visNetwork | visNetwork | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.9 | NA | R (>= 3.0) | htmlwidgets, htmltools, jsonlite, magrittr, utils, methods, grDevices, stats | NA | knitr, rmarkdown, webshot, igraph, rpart, shiny, shinyWidgets, colourpicker, sparkline, ggraph, tidygraph, flashClust | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| visdat | visdat | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.3 | NA | R (>= 3.2.2) | ggplot2, tidyr, dplyr, purrr, readr, magrittr, stats, tibble, glue | NA | testthat, plotly (>= 4.5.6), knitr, rmarkdown, vdiffr, gdtools, spelling | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| vsn | vsn | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 3.52.0 | NA | R (>= 3.4.0), Biobase | methods, affy, limma, lattice, ggplot2 | NA | affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat | NA | Artistic-2.0 | NA | NA | NA | NA | yes | 3.6.1 |
| webshot | webshot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.5.2 | NA | R (>= 3.0) | magrittr, jsonlite, callr | NA | httpuv, knitr, rmarkdown, shiny | NA | GPL-2 | NA | NA | NA | NA | no | 3.6.1 |
| weights | weights | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.1 | NA | Hmisc, gdata, mice | NA | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| whisker | whisker | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.4 | NA | NA | NA | NA | markdown | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.1 |
| whoami | whoami | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.0 | NA | NA | httr, jsonlite, utils | NA | covr, mockery, testthat, withr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| withr | withr | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2.0 | NA | R (>= 3.2.0) | graphics, grDevices, stats | NA | covr, DBI, knitr, lattice, methods, rmarkdown, RSQLite, testthat (>= 2.1.0) | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.2 |
| wskm | wskm | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.4.40 | NA | R (>= 2.10), grDevices, stats, lattice, latticeExtra, fpc | NA | NA | NA | NA | GPL (>= 3) | NA | NA | NA | NA | yes | 3.6.2 |
| xfun | xfun | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.13 | NA | NA | stats, tools | NA | testit, parallel, rstudioapi, tinytex, mime, markdown, knitr, htmltools, base64enc, remotes, rmarkdown | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.2 |
| xgboost | xgboost | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0.2 | NA | R (>= 3.3.0) | Matrix (>= 1.1-0), methods, data.table (>= 1.9.6), magrittr (>= 1.5), stringi (>= 0.5.2) | NA | knitr, rmarkdown, ggplot2 (>= 1.0.1), DiagrammeR (>= 0.9.0), Ckmeans.1d.dp (>= 3.3.1), vcd (>= 1.3), testthat, lintr, igraph (>= 1.0.1), jsonlite, float | NA | Apache License (== 2.0) | file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| xlsx | xlsx | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.3 | NA | NA | rJava, xlsxjars, grDevices, utils | NA | rprojroot, testthat, covr, tibble, knitr, rmarkdown, RefManageR | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.2 |
| xlsxjars | xlsxjars | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.6.1 | NA | rJava | NA | NA | NA | NA | GPL-3 | NA | NA | NA | NA | no | 3.6.0 |
| xml2 | xml2 | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.3.2 | NA | R (>= 3.1.0) | methods | NA | covr, curl, httr, knitr, magrittr, mockery, rmarkdown, testthat (>= 2.1.0) | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| xmlparsedata | xmlparsedata | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.3 | NA | R (>= 3.0.0) | NA | NA | covr, testthat, xml2 | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.1 |
| xopen | xopen | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.0.0 | NA | R (>= 3.1) | processx | NA | ps, testthat | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| xtable | xtable | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8-4 | NA | R (>= 2.10.0) | stats, utils | NA | knitr, plm, zoo, survival | NA | GPL (>= 2) | NA | NA | NA | NA | no | 3.6.0 |
| xts | xts | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.12-0 | NA | zoo (>= 1.7-12) | methods | zoo | timeSeries, timeDate, tseries, chron, fts, tis, RUnit | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| yaml | yaml | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.2.1 | NA | NA | NA | NA | RUnit | NA | BSD_3_clause + file LICENSE | NA | NA | NA | NA | yes | 3.6.2 |
| zeallot | zeallot | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 0.1.0 | NA | NA | NA | NA | testthat, knitr, rmarkdown, purrr, magrittr | NA | MIT + file LICENSE | NA | NA | NA | NA | no | 3.6.0 |
| zip | zip | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 2.0.4 | NA | NA | NA | NA | covr, processx, R6, testthat, withr | NA | CC0 | NA | NA | NA | NA | yes | 3.6.1 |
| zlibbioc | zlibbioc | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.30.0 | NA | NA | NA | NA | NA | NA | Artistic-2.0 + file LICENSE | NA | NA | NA | NA | yes | 3.6.0 |
| zoo | zoo | /home/konrad/R/x86_64-pc-linux-gnu-library/3.6 | 1.8-8 | NA | R (>= 3.1.0), stats | utils, graphics, grDevices, lattice (>= 0.20-27) | NA | AER, coda, chron, fts, ggplot2 (>= 3.0.0), mondate, scales, strucchange, timeDate, timeSeries, tis, tseries, xts | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| BiocManager.1 | BiocManager | /usr/local/lib/R/site-library | 1.30.4 | NA | R (>= 3.5.0) | utils | NA | BiocStyle, BiocVersion, remotes, testthat, knitr, withr | NA | Artistic-2.0 | NA | NA | NA | NA | no | 3.6.1 |
| survival.1 | survival | /usr/local/lib/R/site-library | 2.44-1.1 | recommended | R (>= 2.13.0) | graphics, Matrix, methods, splines, stats, utils | NA | NA | NA | LGPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| KernSmooth | KernSmooth | /usr/lib/R/library | 2.23-17 | recommended | R (>= 2.5.0), stats | NA | NA | MASS | NA | Unlimited | NA | NA | NA | NA | yes | 3.6.2 |
| MASS.1 | MASS | /usr/lib/R/library | 7.3-51.6 | recommended | R (>= 3.1.0), grDevices, graphics, stats, utils | methods | NA | lattice, nlme, nnet, survival | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| Matrix | Matrix | /usr/lib/R/library | 1.2-18 | recommended | R (>= 3.2.0) | methods, graphics, grid, stats, utils, lattice | NA | expm, MASS | MatrixModels, graph, SparseM, sfsmisc | GPL (>= 2) | file LICENCE | NA | NA | NA | NA | yes | 3.6.1 |
| base | base | /usr/lib/R/library | 3.6.2 | base | NA | NA | NA | methods | NA | Part of R 3.6.2 | NA | NA | NA | NA | NA | 3.6.2 |
| boot | boot | /usr/lib/R/library | 1.3-25 | recommended | R (>= 3.0.0), graphics, stats | NA | NA | MASS, survival | NA | Unlimited | NA | NA | NA | NA | no | 3.6.2 |
| class | class | /usr/lib/R/library | 7.3-17 | recommended | R (>= 3.0.0), stats, utils | MASS | NA | NA | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| cluster.1 | cluster | /usr/lib/R/library | 2.1.0 | recommended | R (>= 3.3.0) | graphics, grDevices, stats, utils | NA | MASS, Matrix | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| codetools | codetools | /usr/lib/R/library | 0.2-16 | recommended | R (>= 2.1) | NA | NA | NA | NA | GPL | NA | NA | NA | NA | no | 3.6.0 |
| compiler | compiler | /usr/lib/R/library | 3.6.2 | base | NA | NA | NA | NA | NA | Part of R 3.6.2 | NA | NA | NA | NA | NA | 3.6.2 |
| datasets | datasets | /usr/lib/R/library | 3.6.2 | base | NA | NA | NA | NA | NA | Part of R 3.6.2 | NA | NA | NA | NA | NA | 3.6.2 |
| foreign | foreign | /usr/lib/R/library | 0.8-76 | recommended | R (>= 3.0.0) | methods, utils, stats | NA | NA | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| grDevices | grDevices | /usr/lib/R/library | 3.6.2 | base | NA | NA | NA | KernSmooth | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| graphics | graphics | /usr/lib/R/library | 3.6.2 | base | NA | grDevices | NA | NA | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| grid | grid | /usr/lib/R/library | 3.6.2 | base | NA | grDevices, utils | NA | lattice | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| lattice | lattice | /usr/lib/R/library | 0.20-41 | recommended | R (>= 3.0.0) | grid, grDevices, graphics, stats, utils | NA | KernSmooth, MASS, latticeExtra | chron | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| methods | methods | /usr/lib/R/library | 3.6.2 | base | NA | utils, stats | NA | codetools | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| mgcv.1 | mgcv | /usr/lib/R/library | 1.8-31 | recommended | R (>= 2.14.0), nlme (>= 3.1-64) | methods, stats, graphics, Matrix, splines, utils | NA | parallel, survival, MASS | NA | GPL (>= 2) | NA | NA | NA | NA | yes | 3.6.1 |
| nlme | nlme | /usr/lib/R/library | 3.1-147 | recommended | R (>= 3.4.0) | graphics, stats, utils, lattice | NA | Hmisc, MASS | NA | GPL (>= 2) | file LICENCE | NA | NA | NA | NA | yes | 3.6.2 |
| nnet | nnet | /usr/lib/R/library | 7.3-14 | recommended | R (>= 3.0.0), stats, utils | NA | NA | MASS | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| parallel | parallel | /usr/lib/R/library | 3.6.2 | base | NA | tools, compiler | NA | methods | snow, nws, Rmpi | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| rpart.1 | rpart | /usr/lib/R/library | 4.1-15 | recommended | R (>= 2.15.0), graphics, stats, grDevices | NA | NA | survival | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.1 |
| spatial | spatial | /usr/lib/R/library | 7.3-12 | recommended | R (>= 3.0.0), graphics, stats, utils | NA | NA | MASS | NA | GPL-2 | GPL-3 | NA | NA | NA | NA | yes | 3.6.2 |
| splines | splines | /usr/lib/R/library | 3.6.2 | base | NA | graphics, stats | NA | Matrix, methods | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| stats | stats | /usr/lib/R/library | 3.6.2 | base | NA | utils, grDevices, graphics | NA | MASS, Matrix, SuppDists, methods, stats4 | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| stats4 | stats4 | /usr/lib/R/library | 3.6.2 | base | NA | graphics, methods, stats | NA | NA | NA | Part of R 3.6.2 | NA | NA | NA | NA | NA | 3.6.2 |
| survival.2 | survival | /usr/lib/R/library | 3.1-8 | recommended | R (>= 3.4.0) | graphics, Matrix, methods, splines, stats, utils | NA | NA | NA | LGPL (>= 2) | NA | NA | NA | NA | yes | 3.6.2 |
| tcltk | tcltk | /usr/lib/R/library | 3.6.2 | base | NA | utils | NA | NA | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| tools | tools | /usr/lib/R/library | 3.6.2 | base | NA | NA | NA | codetools, methods, xml2, curl, commonmark | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |
| utils | utils | /usr/lib/R/library | 3.6.2 | base | NA | NA | NA | methods, xml2, commonmark | NA | Part of R 3.6.2 | NA | NA | NA | NA | yes | 3.6.2 |